python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split0 0 1 2 100 hg38.150200.bed.split0.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1 0 1 2 100 hg38.150200.bed.split1.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10 0 1 2 100 hg38.150200.bed.split10.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split100 0 1 2 100 hg38.150200.bed.split100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1000 0 1 2 100 hg38.150200.bed.split1000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10000 0 1 2 100 hg38.150200.bed.split10000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10001 0 1 2 100 hg38.150200.bed.split10001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10002 0 1 2 100 hg38.150200.bed.split10002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10003 0 1 2 100 hg38.150200.bed.split10003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10004 0 1 2 100 hg38.150200.bed.split10004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10005 0 1 2 100 hg38.150200.bed.split10005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10006 0 1 2 100 hg38.150200.bed.split10006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10007 0 1 2 100 hg38.150200.bed.split10007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10008 0 1 2 100 hg38.150200.bed.split10008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10009 0 1 2 100 hg38.150200.bed.split10009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1001 0 1 2 100 hg38.150200.bed.split1001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10010 0 1 2 100 hg38.150200.bed.split10010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10011 0 1 2 100 hg38.150200.bed.split10011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10012 0 1 2 100 hg38.150200.bed.split10012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10013 0 1 2 100 hg38.150200.bed.split10013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10014 0 1 2 100 hg38.150200.bed.split10014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10015 0 1 2 100 hg38.150200.bed.split10015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10016 0 1 2 100 hg38.150200.bed.split10016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10017 0 1 2 100 hg38.150200.bed.split10017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10018 0 1 2 100 hg38.150200.bed.split10018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10019 0 1 2 100 hg38.150200.bed.split10019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1002 0 1 2 100 hg38.150200.bed.split1002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10020 0 1 2 100 hg38.150200.bed.split10020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10021 0 1 2 100 hg38.150200.bed.split10021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10022 0 1 2 100 hg38.150200.bed.split10022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10023 0 1 2 100 hg38.150200.bed.split10023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10024 0 1 2 100 hg38.150200.bed.split10024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10025 0 1 2 100 hg38.150200.bed.split10025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10026 0 1 2 100 hg38.150200.bed.split10026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10027 0 1 2 100 hg38.150200.bed.split10027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10028 0 1 2 100 hg38.150200.bed.split10028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10029 0 1 2 100 hg38.150200.bed.split10029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1003 0 1 2 100 hg38.150200.bed.split1003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10030 0 1 2 100 hg38.150200.bed.split10030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10031 0 1 2 100 hg38.150200.bed.split10031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10032 0 1 2 100 hg38.150200.bed.split10032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10033 0 1 2 100 hg38.150200.bed.split10033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10034 0 1 2 100 hg38.150200.bed.split10034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10035 0 1 2 100 hg38.150200.bed.split10035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10036 0 1 2 100 hg38.150200.bed.split10036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10037 0 1 2 100 hg38.150200.bed.split10037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10038 0 1 2 100 hg38.150200.bed.split10038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10039 0 1 2 100 hg38.150200.bed.split10039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1004 0 1 2 100 hg38.150200.bed.split1004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10040 0 1 2 100 hg38.150200.bed.split10040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10041 0 1 2 100 hg38.150200.bed.split10041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10042 0 1 2 100 hg38.150200.bed.split10042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10043 0 1 2 100 hg38.150200.bed.split10043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10044 0 1 2 100 hg38.150200.bed.split10044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10045 0 1 2 100 hg38.150200.bed.split10045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10046 0 1 2 100 hg38.150200.bed.split10046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10047 0 1 2 100 hg38.150200.bed.split10047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10048 0 1 2 100 hg38.150200.bed.split10048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10049 0 1 2 100 hg38.150200.bed.split10049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1005 0 1 2 100 hg38.150200.bed.split1005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10050 0 1 2 100 hg38.150200.bed.split10050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10051 0 1 2 100 hg38.150200.bed.split10051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10052 0 1 2 100 hg38.150200.bed.split10052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10053 0 1 2 100 hg38.150200.bed.split10053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10054 0 1 2 100 hg38.150200.bed.split10054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10055 0 1 2 100 hg38.150200.bed.split10055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10056 0 1 2 100 hg38.150200.bed.split10056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10057 0 1 2 100 hg38.150200.bed.split10057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10058 0 1 2 100 hg38.150200.bed.split10058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10059 0 1 2 100 hg38.150200.bed.split10059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1006 0 1 2 100 hg38.150200.bed.split1006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10060 0 1 2 100 hg38.150200.bed.split10060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10061 0 1 2 100 hg38.150200.bed.split10061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10062 0 1 2 100 hg38.150200.bed.split10062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10063 0 1 2 100 hg38.150200.bed.split10063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10064 0 1 2 100 hg38.150200.bed.split10064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10065 0 1 2 100 hg38.150200.bed.split10065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10066 0 1 2 100 hg38.150200.bed.split10066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10067 0 1 2 100 hg38.150200.bed.split10067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10068 0 1 2 100 hg38.150200.bed.split10068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10069 0 1 2 100 hg38.150200.bed.split10069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1007 0 1 2 100 hg38.150200.bed.split1007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10070 0 1 2 100 hg38.150200.bed.split10070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10071 0 1 2 100 hg38.150200.bed.split10071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10072 0 1 2 100 hg38.150200.bed.split10072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10073 0 1 2 100 hg38.150200.bed.split10073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10074 0 1 2 100 hg38.150200.bed.split10074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10075 0 1 2 100 hg38.150200.bed.split10075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10076 0 1 2 100 hg38.150200.bed.split10076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10077 0 1 2 100 hg38.150200.bed.split10077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10078 0 1 2 100 hg38.150200.bed.split10078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10079 0 1 2 100 hg38.150200.bed.split10079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1008 0 1 2 100 hg38.150200.bed.split1008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10080 0 1 2 100 hg38.150200.bed.split10080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10081 0 1 2 100 hg38.150200.bed.split10081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10082 0 1 2 100 hg38.150200.bed.split10082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10083 0 1 2 100 hg38.150200.bed.split10083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10084 0 1 2 100 hg38.150200.bed.split10084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10085 0 1 2 100 hg38.150200.bed.split10085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10086 0 1 2 100 hg38.150200.bed.split10086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10087 0 1 2 100 hg38.150200.bed.split10087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10088 0 1 2 100 hg38.150200.bed.split10088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10089 0 1 2 100 hg38.150200.bed.split10089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1009 0 1 2 100 hg38.150200.bed.split1009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10090 0 1 2 100 hg38.150200.bed.split10090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10091 0 1 2 100 hg38.150200.bed.split10091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10092 0 1 2 100 hg38.150200.bed.split10092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10093 0 1 2 100 hg38.150200.bed.split10093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10094 0 1 2 100 hg38.150200.bed.split10094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10095 0 1 2 100 hg38.150200.bed.split10095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10096 0 1 2 100 hg38.150200.bed.split10096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10097 0 1 2 100 hg38.150200.bed.split10097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10098 0 1 2 100 hg38.150200.bed.split10098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10099 0 1 2 100 hg38.150200.bed.split10099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split101 0 1 2 100 hg38.150200.bed.split101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1010 0 1 2 100 hg38.150200.bed.split1010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10100 0 1 2 100 hg38.150200.bed.split10100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10101 0 1 2 100 hg38.150200.bed.split10101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10102 0 1 2 100 hg38.150200.bed.split10102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10103 0 1 2 100 hg38.150200.bed.split10103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10104 0 1 2 100 hg38.150200.bed.split10104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10105 0 1 2 100 hg38.150200.bed.split10105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10106 0 1 2 100 hg38.150200.bed.split10106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10107 0 1 2 100 hg38.150200.bed.split10107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10108 0 1 2 100 hg38.150200.bed.split10108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10109 0 1 2 100 hg38.150200.bed.split10109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1011 0 1 2 100 hg38.150200.bed.split1011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10110 0 1 2 100 hg38.150200.bed.split10110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10111 0 1 2 100 hg38.150200.bed.split10111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10112 0 1 2 100 hg38.150200.bed.split10112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10113 0 1 2 100 hg38.150200.bed.split10113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10114 0 1 2 100 hg38.150200.bed.split10114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10115 0 1 2 100 hg38.150200.bed.split10115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10116 0 1 2 100 hg38.150200.bed.split10116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10117 0 1 2 100 hg38.150200.bed.split10117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10118 0 1 2 100 hg38.150200.bed.split10118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10119 0 1 2 100 hg38.150200.bed.split10119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1012 0 1 2 100 hg38.150200.bed.split1012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10120 0 1 2 100 hg38.150200.bed.split10120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10121 0 1 2 100 hg38.150200.bed.split10121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10122 0 1 2 100 hg38.150200.bed.split10122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10123 0 1 2 100 hg38.150200.bed.split10123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10124 0 1 2 100 hg38.150200.bed.split10124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10125 0 1 2 100 hg38.150200.bed.split10125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10126 0 1 2 100 hg38.150200.bed.split10126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10127 0 1 2 100 hg38.150200.bed.split10127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10128 0 1 2 100 hg38.150200.bed.split10128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10129 0 1 2 100 hg38.150200.bed.split10129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1013 0 1 2 100 hg38.150200.bed.split1013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10130 0 1 2 100 hg38.150200.bed.split10130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10131 0 1 2 100 hg38.150200.bed.split10131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10132 0 1 2 100 hg38.150200.bed.split10132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10133 0 1 2 100 hg38.150200.bed.split10133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10134 0 1 2 100 hg38.150200.bed.split10134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10135 0 1 2 100 hg38.150200.bed.split10135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10136 0 1 2 100 hg38.150200.bed.split10136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10137 0 1 2 100 hg38.150200.bed.split10137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10138 0 1 2 100 hg38.150200.bed.split10138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10139 0 1 2 100 hg38.150200.bed.split10139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1014 0 1 2 100 hg38.150200.bed.split1014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10140 0 1 2 100 hg38.150200.bed.split10140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10141 0 1 2 100 hg38.150200.bed.split10141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10142 0 1 2 100 hg38.150200.bed.split10142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10143 0 1 2 100 hg38.150200.bed.split10143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10144 0 1 2 100 hg38.150200.bed.split10144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10145 0 1 2 100 hg38.150200.bed.split10145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10146 0 1 2 100 hg38.150200.bed.split10146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10147 0 1 2 100 hg38.150200.bed.split10147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10148 0 1 2 100 hg38.150200.bed.split10148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10149 0 1 2 100 hg38.150200.bed.split10149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1015 0 1 2 100 hg38.150200.bed.split1015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10150 0 1 2 100 hg38.150200.bed.split10150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10151 0 1 2 100 hg38.150200.bed.split10151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10152 0 1 2 100 hg38.150200.bed.split10152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10153 0 1 2 100 hg38.150200.bed.split10153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10154 0 1 2 100 hg38.150200.bed.split10154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10155 0 1 2 100 hg38.150200.bed.split10155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10156 0 1 2 100 hg38.150200.bed.split10156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10157 0 1 2 100 hg38.150200.bed.split10157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10158 0 1 2 100 hg38.150200.bed.split10158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10159 0 1 2 100 hg38.150200.bed.split10159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1016 0 1 2 100 hg38.150200.bed.split1016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10160 0 1 2 100 hg38.150200.bed.split10160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10161 0 1 2 100 hg38.150200.bed.split10161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10162 0 1 2 100 hg38.150200.bed.split10162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10163 0 1 2 100 hg38.150200.bed.split10163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10164 0 1 2 100 hg38.150200.bed.split10164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10165 0 1 2 100 hg38.150200.bed.split10165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10166 0 1 2 100 hg38.150200.bed.split10166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10167 0 1 2 100 hg38.150200.bed.split10167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10168 0 1 2 100 hg38.150200.bed.split10168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10169 0 1 2 100 hg38.150200.bed.split10169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1017 0 1 2 100 hg38.150200.bed.split1017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10170 0 1 2 100 hg38.150200.bed.split10170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10171 0 1 2 100 hg38.150200.bed.split10171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10172 0 1 2 100 hg38.150200.bed.split10172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10173 0 1 2 100 hg38.150200.bed.split10173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10174 0 1 2 100 hg38.150200.bed.split10174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10175 0 1 2 100 hg38.150200.bed.split10175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10176 0 1 2 100 hg38.150200.bed.split10176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10177 0 1 2 100 hg38.150200.bed.split10177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10178 0 1 2 100 hg38.150200.bed.split10178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10179 0 1 2 100 hg38.150200.bed.split10179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1018 0 1 2 100 hg38.150200.bed.split1018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10180 0 1 2 100 hg38.150200.bed.split10180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10181 0 1 2 100 hg38.150200.bed.split10181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10182 0 1 2 100 hg38.150200.bed.split10182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10183 0 1 2 100 hg38.150200.bed.split10183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10184 0 1 2 100 hg38.150200.bed.split10184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10185 0 1 2 100 hg38.150200.bed.split10185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10186 0 1 2 100 hg38.150200.bed.split10186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10187 0 1 2 100 hg38.150200.bed.split10187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10188 0 1 2 100 hg38.150200.bed.split10188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10189 0 1 2 100 hg38.150200.bed.split10189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1019 0 1 2 100 hg38.150200.bed.split1019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10190 0 1 2 100 hg38.150200.bed.split10190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10191 0 1 2 100 hg38.150200.bed.split10191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10192 0 1 2 100 hg38.150200.bed.split10192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10193 0 1 2 100 hg38.150200.bed.split10193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10194 0 1 2 100 hg38.150200.bed.split10194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10195 0 1 2 100 hg38.150200.bed.split10195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10196 0 1 2 100 hg38.150200.bed.split10196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10197 0 1 2 100 hg38.150200.bed.split10197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10198 0 1 2 100 hg38.150200.bed.split10198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10199 0 1 2 100 hg38.150200.bed.split10199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split102 0 1 2 100 hg38.150200.bed.split102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1020 0 1 2 100 hg38.150200.bed.split1020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10200 0 1 2 100 hg38.150200.bed.split10200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10201 0 1 2 100 hg38.150200.bed.split10201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10202 0 1 2 100 hg38.150200.bed.split10202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10203 0 1 2 100 hg38.150200.bed.split10203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10204 0 1 2 100 hg38.150200.bed.split10204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10205 0 1 2 100 hg38.150200.bed.split10205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10206 0 1 2 100 hg38.150200.bed.split10206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10207 0 1 2 100 hg38.150200.bed.split10207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10208 0 1 2 100 hg38.150200.bed.split10208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10209 0 1 2 100 hg38.150200.bed.split10209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1021 0 1 2 100 hg38.150200.bed.split1021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10210 0 1 2 100 hg38.150200.bed.split10210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10211 0 1 2 100 hg38.150200.bed.split10211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10212 0 1 2 100 hg38.150200.bed.split10212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10213 0 1 2 100 hg38.150200.bed.split10213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10214 0 1 2 100 hg38.150200.bed.split10214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10215 0 1 2 100 hg38.150200.bed.split10215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10216 0 1 2 100 hg38.150200.bed.split10216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10217 0 1 2 100 hg38.150200.bed.split10217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10218 0 1 2 100 hg38.150200.bed.split10218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10219 0 1 2 100 hg38.150200.bed.split10219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1022 0 1 2 100 hg38.150200.bed.split1022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10220 0 1 2 100 hg38.150200.bed.split10220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10221 0 1 2 100 hg38.150200.bed.split10221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10222 0 1 2 100 hg38.150200.bed.split10222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10223 0 1 2 100 hg38.150200.bed.split10223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10224 0 1 2 100 hg38.150200.bed.split10224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10225 0 1 2 100 hg38.150200.bed.split10225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10226 0 1 2 100 hg38.150200.bed.split10226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10227 0 1 2 100 hg38.150200.bed.split10227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10228 0 1 2 100 hg38.150200.bed.split10228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10229 0 1 2 100 hg38.150200.bed.split10229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1023 0 1 2 100 hg38.150200.bed.split1023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10230 0 1 2 100 hg38.150200.bed.split10230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10231 0 1 2 100 hg38.150200.bed.split10231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10232 0 1 2 100 hg38.150200.bed.split10232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10233 0 1 2 100 hg38.150200.bed.split10233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10234 0 1 2 100 hg38.150200.bed.split10234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10235 0 1 2 100 hg38.150200.bed.split10235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10236 0 1 2 100 hg38.150200.bed.split10236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10237 0 1 2 100 hg38.150200.bed.split10237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10238 0 1 2 100 hg38.150200.bed.split10238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10239 0 1 2 100 hg38.150200.bed.split10239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1024 0 1 2 100 hg38.150200.bed.split1024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10240 0 1 2 100 hg38.150200.bed.split10240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10241 0 1 2 100 hg38.150200.bed.split10241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10242 0 1 2 100 hg38.150200.bed.split10242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10243 0 1 2 100 hg38.150200.bed.split10243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10244 0 1 2 100 hg38.150200.bed.split10244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10245 0 1 2 100 hg38.150200.bed.split10245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10246 0 1 2 100 hg38.150200.bed.split10246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10247 0 1 2 100 hg38.150200.bed.split10247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10248 0 1 2 100 hg38.150200.bed.split10248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10249 0 1 2 100 hg38.150200.bed.split10249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1025 0 1 2 100 hg38.150200.bed.split1025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10250 0 1 2 100 hg38.150200.bed.split10250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10251 0 1 2 100 hg38.150200.bed.split10251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10252 0 1 2 100 hg38.150200.bed.split10252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10253 0 1 2 100 hg38.150200.bed.split10253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10254 0 1 2 100 hg38.150200.bed.split10254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10255 0 1 2 100 hg38.150200.bed.split10255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10256 0 1 2 100 hg38.150200.bed.split10256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10257 0 1 2 100 hg38.150200.bed.split10257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10258 0 1 2 100 hg38.150200.bed.split10258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10259 0 1 2 100 hg38.150200.bed.split10259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1026 0 1 2 100 hg38.150200.bed.split1026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10260 0 1 2 100 hg38.150200.bed.split10260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10261 0 1 2 100 hg38.150200.bed.split10261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10262 0 1 2 100 hg38.150200.bed.split10262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10263 0 1 2 100 hg38.150200.bed.split10263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10264 0 1 2 100 hg38.150200.bed.split10264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10265 0 1 2 100 hg38.150200.bed.split10265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10266 0 1 2 100 hg38.150200.bed.split10266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10267 0 1 2 100 hg38.150200.bed.split10267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10268 0 1 2 100 hg38.150200.bed.split10268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10269 0 1 2 100 hg38.150200.bed.split10269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1027 0 1 2 100 hg38.150200.bed.split1027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10270 0 1 2 100 hg38.150200.bed.split10270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10271 0 1 2 100 hg38.150200.bed.split10271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10272 0 1 2 100 hg38.150200.bed.split10272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10273 0 1 2 100 hg38.150200.bed.split10273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10274 0 1 2 100 hg38.150200.bed.split10274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10275 0 1 2 100 hg38.150200.bed.split10275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10276 0 1 2 100 hg38.150200.bed.split10276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10277 0 1 2 100 hg38.150200.bed.split10277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10278 0 1 2 100 hg38.150200.bed.split10278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10279 0 1 2 100 hg38.150200.bed.split10279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1028 0 1 2 100 hg38.150200.bed.split1028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10280 0 1 2 100 hg38.150200.bed.split10280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10281 0 1 2 100 hg38.150200.bed.split10281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10282 0 1 2 100 hg38.150200.bed.split10282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10283 0 1 2 100 hg38.150200.bed.split10283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10284 0 1 2 100 hg38.150200.bed.split10284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10285 0 1 2 100 hg38.150200.bed.split10285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10286 0 1 2 100 hg38.150200.bed.split10286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10287 0 1 2 100 hg38.150200.bed.split10287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10288 0 1 2 100 hg38.150200.bed.split10288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10289 0 1 2 100 hg38.150200.bed.split10289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1029 0 1 2 100 hg38.150200.bed.split1029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10290 0 1 2 100 hg38.150200.bed.split10290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10291 0 1 2 100 hg38.150200.bed.split10291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10292 0 1 2 100 hg38.150200.bed.split10292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10293 0 1 2 100 hg38.150200.bed.split10293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10294 0 1 2 100 hg38.150200.bed.split10294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10295 0 1 2 100 hg38.150200.bed.split10295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10296 0 1 2 100 hg38.150200.bed.split10296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10297 0 1 2 100 hg38.150200.bed.split10297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10298 0 1 2 100 hg38.150200.bed.split10298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10299 0 1 2 100 hg38.150200.bed.split10299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split103 0 1 2 100 hg38.150200.bed.split103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1030 0 1 2 100 hg38.150200.bed.split1030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10300 0 1 2 100 hg38.150200.bed.split10300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10301 0 1 2 100 hg38.150200.bed.split10301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10302 0 1 2 100 hg38.150200.bed.split10302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10303 0 1 2 100 hg38.150200.bed.split10303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10304 0 1 2 100 hg38.150200.bed.split10304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10305 0 1 2 100 hg38.150200.bed.split10305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10306 0 1 2 100 hg38.150200.bed.split10306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10307 0 1 2 100 hg38.150200.bed.split10307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10308 0 1 2 100 hg38.150200.bed.split10308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10309 0 1 2 100 hg38.150200.bed.split10309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1031 0 1 2 100 hg38.150200.bed.split1031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10310 0 1 2 100 hg38.150200.bed.split10310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10311 0 1 2 100 hg38.150200.bed.split10311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10312 0 1 2 100 hg38.150200.bed.split10312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10313 0 1 2 100 hg38.150200.bed.split10313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10314 0 1 2 100 hg38.150200.bed.split10314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10315 0 1 2 100 hg38.150200.bed.split10315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10316 0 1 2 100 hg38.150200.bed.split10316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10317 0 1 2 100 hg38.150200.bed.split10317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10318 0 1 2 100 hg38.150200.bed.split10318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10319 0 1 2 100 hg38.150200.bed.split10319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1032 0 1 2 100 hg38.150200.bed.split1032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10320 0 1 2 100 hg38.150200.bed.split10320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10321 0 1 2 100 hg38.150200.bed.split10321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10322 0 1 2 100 hg38.150200.bed.split10322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10323 0 1 2 100 hg38.150200.bed.split10323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10324 0 1 2 100 hg38.150200.bed.split10324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10325 0 1 2 100 hg38.150200.bed.split10325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10326 0 1 2 100 hg38.150200.bed.split10326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10327 0 1 2 100 hg38.150200.bed.split10327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10328 0 1 2 100 hg38.150200.bed.split10328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10329 0 1 2 100 hg38.150200.bed.split10329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1033 0 1 2 100 hg38.150200.bed.split1033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10330 0 1 2 100 hg38.150200.bed.split10330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10331 0 1 2 100 hg38.150200.bed.split10331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10332 0 1 2 100 hg38.150200.bed.split10332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10333 0 1 2 100 hg38.150200.bed.split10333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10334 0 1 2 100 hg38.150200.bed.split10334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10335 0 1 2 100 hg38.150200.bed.split10335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10336 0 1 2 100 hg38.150200.bed.split10336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10337 0 1 2 100 hg38.150200.bed.split10337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10338 0 1 2 100 hg38.150200.bed.split10338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10339 0 1 2 100 hg38.150200.bed.split10339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1034 0 1 2 100 hg38.150200.bed.split1034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10340 0 1 2 100 hg38.150200.bed.split10340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10341 0 1 2 100 hg38.150200.bed.split10341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10342 0 1 2 100 hg38.150200.bed.split10342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10343 0 1 2 100 hg38.150200.bed.split10343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10344 0 1 2 100 hg38.150200.bed.split10344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10345 0 1 2 100 hg38.150200.bed.split10345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10346 0 1 2 100 hg38.150200.bed.split10346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10347 0 1 2 100 hg38.150200.bed.split10347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10348 0 1 2 100 hg38.150200.bed.split10348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10349 0 1 2 100 hg38.150200.bed.split10349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1035 0 1 2 100 hg38.150200.bed.split1035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10350 0 1 2 100 hg38.150200.bed.split10350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10351 0 1 2 100 hg38.150200.bed.split10351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10352 0 1 2 100 hg38.150200.bed.split10352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10353 0 1 2 100 hg38.150200.bed.split10353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10354 0 1 2 100 hg38.150200.bed.split10354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10355 0 1 2 100 hg38.150200.bed.split10355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10356 0 1 2 100 hg38.150200.bed.split10356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10357 0 1 2 100 hg38.150200.bed.split10357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10358 0 1 2 100 hg38.150200.bed.split10358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10359 0 1 2 100 hg38.150200.bed.split10359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1036 0 1 2 100 hg38.150200.bed.split1036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10360 0 1 2 100 hg38.150200.bed.split10360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10361 0 1 2 100 hg38.150200.bed.split10361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10362 0 1 2 100 hg38.150200.bed.split10362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10363 0 1 2 100 hg38.150200.bed.split10363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10364 0 1 2 100 hg38.150200.bed.split10364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10365 0 1 2 100 hg38.150200.bed.split10365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10366 0 1 2 100 hg38.150200.bed.split10366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10367 0 1 2 100 hg38.150200.bed.split10367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10368 0 1 2 100 hg38.150200.bed.split10368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10369 0 1 2 100 hg38.150200.bed.split10369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1037 0 1 2 100 hg38.150200.bed.split1037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10370 0 1 2 100 hg38.150200.bed.split10370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10371 0 1 2 100 hg38.150200.bed.split10371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10372 0 1 2 100 hg38.150200.bed.split10372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10373 0 1 2 100 hg38.150200.bed.split10373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10374 0 1 2 100 hg38.150200.bed.split10374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10375 0 1 2 100 hg38.150200.bed.split10375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10376 0 1 2 100 hg38.150200.bed.split10376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10377 0 1 2 100 hg38.150200.bed.split10377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10378 0 1 2 100 hg38.150200.bed.split10378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10379 0 1 2 100 hg38.150200.bed.split10379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1038 0 1 2 100 hg38.150200.bed.split1038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10380 0 1 2 100 hg38.150200.bed.split10380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10381 0 1 2 100 hg38.150200.bed.split10381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10382 0 1 2 100 hg38.150200.bed.split10382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10383 0 1 2 100 hg38.150200.bed.split10383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10384 0 1 2 100 hg38.150200.bed.split10384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10385 0 1 2 100 hg38.150200.bed.split10385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10386 0 1 2 100 hg38.150200.bed.split10386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10387 0 1 2 100 hg38.150200.bed.split10387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10388 0 1 2 100 hg38.150200.bed.split10388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10389 0 1 2 100 hg38.150200.bed.split10389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1039 0 1 2 100 hg38.150200.bed.split1039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10390 0 1 2 100 hg38.150200.bed.split10390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10391 0 1 2 100 hg38.150200.bed.split10391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10392 0 1 2 100 hg38.150200.bed.split10392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10393 0 1 2 100 hg38.150200.bed.split10393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10394 0 1 2 100 hg38.150200.bed.split10394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10395 0 1 2 100 hg38.150200.bed.split10395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10396 0 1 2 100 hg38.150200.bed.split10396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10397 0 1 2 100 hg38.150200.bed.split10397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10398 0 1 2 100 hg38.150200.bed.split10398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10399 0 1 2 100 hg38.150200.bed.split10399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split104 0 1 2 100 hg38.150200.bed.split104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1040 0 1 2 100 hg38.150200.bed.split1040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10400 0 1 2 100 hg38.150200.bed.split10400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10401 0 1 2 100 hg38.150200.bed.split10401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10402 0 1 2 100 hg38.150200.bed.split10402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10403 0 1 2 100 hg38.150200.bed.split10403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10404 0 1 2 100 hg38.150200.bed.split10404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10405 0 1 2 100 hg38.150200.bed.split10405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10406 0 1 2 100 hg38.150200.bed.split10406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10407 0 1 2 100 hg38.150200.bed.split10407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10408 0 1 2 100 hg38.150200.bed.split10408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10409 0 1 2 100 hg38.150200.bed.split10409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1041 0 1 2 100 hg38.150200.bed.split1041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10410 0 1 2 100 hg38.150200.bed.split10410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10411 0 1 2 100 hg38.150200.bed.split10411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10412 0 1 2 100 hg38.150200.bed.split10412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10413 0 1 2 100 hg38.150200.bed.split10413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10414 0 1 2 100 hg38.150200.bed.split10414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10415 0 1 2 100 hg38.150200.bed.split10415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10416 0 1 2 100 hg38.150200.bed.split10416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10417 0 1 2 100 hg38.150200.bed.split10417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10418 0 1 2 100 hg38.150200.bed.split10418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10419 0 1 2 100 hg38.150200.bed.split10419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1042 0 1 2 100 hg38.150200.bed.split1042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10420 0 1 2 100 hg38.150200.bed.split10420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10421 0 1 2 100 hg38.150200.bed.split10421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10422 0 1 2 100 hg38.150200.bed.split10422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10423 0 1 2 100 hg38.150200.bed.split10423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10424 0 1 2 100 hg38.150200.bed.split10424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10425 0 1 2 100 hg38.150200.bed.split10425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10426 0 1 2 100 hg38.150200.bed.split10426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10427 0 1 2 100 hg38.150200.bed.split10427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10428 0 1 2 100 hg38.150200.bed.split10428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10429 0 1 2 100 hg38.150200.bed.split10429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1043 0 1 2 100 hg38.150200.bed.split1043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10430 0 1 2 100 hg38.150200.bed.split10430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10431 0 1 2 100 hg38.150200.bed.split10431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10432 0 1 2 100 hg38.150200.bed.split10432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10433 0 1 2 100 hg38.150200.bed.split10433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10434 0 1 2 100 hg38.150200.bed.split10434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10435 0 1 2 100 hg38.150200.bed.split10435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10436 0 1 2 100 hg38.150200.bed.split10436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10437 0 1 2 100 hg38.150200.bed.split10437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10438 0 1 2 100 hg38.150200.bed.split10438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10439 0 1 2 100 hg38.150200.bed.split10439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1044 0 1 2 100 hg38.150200.bed.split1044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10440 0 1 2 100 hg38.150200.bed.split10440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10441 0 1 2 100 hg38.150200.bed.split10441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10442 0 1 2 100 hg38.150200.bed.split10442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10443 0 1 2 100 hg38.150200.bed.split10443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10444 0 1 2 100 hg38.150200.bed.split10444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10445 0 1 2 100 hg38.150200.bed.split10445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10446 0 1 2 100 hg38.150200.bed.split10446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10447 0 1 2 100 hg38.150200.bed.split10447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10448 0 1 2 100 hg38.150200.bed.split10448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10449 0 1 2 100 hg38.150200.bed.split10449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1045 0 1 2 100 hg38.150200.bed.split1045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10450 0 1 2 100 hg38.150200.bed.split10450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10451 0 1 2 100 hg38.150200.bed.split10451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10452 0 1 2 100 hg38.150200.bed.split10452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10453 0 1 2 100 hg38.150200.bed.split10453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10454 0 1 2 100 hg38.150200.bed.split10454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10455 0 1 2 100 hg38.150200.bed.split10455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10456 0 1 2 100 hg38.150200.bed.split10456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10457 0 1 2 100 hg38.150200.bed.split10457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10458 0 1 2 100 hg38.150200.bed.split10458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10459 0 1 2 100 hg38.150200.bed.split10459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1046 0 1 2 100 hg38.150200.bed.split1046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10460 0 1 2 100 hg38.150200.bed.split10460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10461 0 1 2 100 hg38.150200.bed.split10461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10462 0 1 2 100 hg38.150200.bed.split10462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10463 0 1 2 100 hg38.150200.bed.split10463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10464 0 1 2 100 hg38.150200.bed.split10464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10465 0 1 2 100 hg38.150200.bed.split10465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10466 0 1 2 100 hg38.150200.bed.split10466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10467 0 1 2 100 hg38.150200.bed.split10467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10468 0 1 2 100 hg38.150200.bed.split10468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10469 0 1 2 100 hg38.150200.bed.split10469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1047 0 1 2 100 hg38.150200.bed.split1047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10470 0 1 2 100 hg38.150200.bed.split10470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10471 0 1 2 100 hg38.150200.bed.split10471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10472 0 1 2 100 hg38.150200.bed.split10472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10473 0 1 2 100 hg38.150200.bed.split10473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10474 0 1 2 100 hg38.150200.bed.split10474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10475 0 1 2 100 hg38.150200.bed.split10475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10476 0 1 2 100 hg38.150200.bed.split10476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10477 0 1 2 100 hg38.150200.bed.split10477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10478 0 1 2 100 hg38.150200.bed.split10478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10479 0 1 2 100 hg38.150200.bed.split10479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1048 0 1 2 100 hg38.150200.bed.split1048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10480 0 1 2 100 hg38.150200.bed.split10480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10481 0 1 2 100 hg38.150200.bed.split10481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10482 0 1 2 100 hg38.150200.bed.split10482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10483 0 1 2 100 hg38.150200.bed.split10483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10484 0 1 2 100 hg38.150200.bed.split10484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10485 0 1 2 100 hg38.150200.bed.split10485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10486 0 1 2 100 hg38.150200.bed.split10486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10487 0 1 2 100 hg38.150200.bed.split10487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10488 0 1 2 100 hg38.150200.bed.split10488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10489 0 1 2 100 hg38.150200.bed.split10489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1049 0 1 2 100 hg38.150200.bed.split1049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10490 0 1 2 100 hg38.150200.bed.split10490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10491 0 1 2 100 hg38.150200.bed.split10491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10492 0 1 2 100 hg38.150200.bed.split10492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10493 0 1 2 100 hg38.150200.bed.split10493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10494 0 1 2 100 hg38.150200.bed.split10494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10495 0 1 2 100 hg38.150200.bed.split10495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10496 0 1 2 100 hg38.150200.bed.split10496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10497 0 1 2 100 hg38.150200.bed.split10497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10498 0 1 2 100 hg38.150200.bed.split10498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10499 0 1 2 100 hg38.150200.bed.split10499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split105 0 1 2 100 hg38.150200.bed.split105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1050 0 1 2 100 hg38.150200.bed.split1050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10500 0 1 2 100 hg38.150200.bed.split10500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10501 0 1 2 100 hg38.150200.bed.split10501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10502 0 1 2 100 hg38.150200.bed.split10502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10503 0 1 2 100 hg38.150200.bed.split10503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10504 0 1 2 100 hg38.150200.bed.split10504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10505 0 1 2 100 hg38.150200.bed.split10505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10506 0 1 2 100 hg38.150200.bed.split10506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10507 0 1 2 100 hg38.150200.bed.split10507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10508 0 1 2 100 hg38.150200.bed.split10508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10509 0 1 2 100 hg38.150200.bed.split10509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1051 0 1 2 100 hg38.150200.bed.split1051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10510 0 1 2 100 hg38.150200.bed.split10510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10511 0 1 2 100 hg38.150200.bed.split10511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10512 0 1 2 100 hg38.150200.bed.split10512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10513 0 1 2 100 hg38.150200.bed.split10513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10514 0 1 2 100 hg38.150200.bed.split10514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10515 0 1 2 100 hg38.150200.bed.split10515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10516 0 1 2 100 hg38.150200.bed.split10516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10517 0 1 2 100 hg38.150200.bed.split10517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10518 0 1 2 100 hg38.150200.bed.split10518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10519 0 1 2 100 hg38.150200.bed.split10519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1052 0 1 2 100 hg38.150200.bed.split1052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10520 0 1 2 100 hg38.150200.bed.split10520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10521 0 1 2 100 hg38.150200.bed.split10521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10522 0 1 2 100 hg38.150200.bed.split10522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10523 0 1 2 100 hg38.150200.bed.split10523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10524 0 1 2 100 hg38.150200.bed.split10524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10525 0 1 2 100 hg38.150200.bed.split10525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10526 0 1 2 100 hg38.150200.bed.split10526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10527 0 1 2 100 hg38.150200.bed.split10527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10528 0 1 2 100 hg38.150200.bed.split10528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10529 0 1 2 100 hg38.150200.bed.split10529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1053 0 1 2 100 hg38.150200.bed.split1053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10530 0 1 2 100 hg38.150200.bed.split10530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10531 0 1 2 100 hg38.150200.bed.split10531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10532 0 1 2 100 hg38.150200.bed.split10532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10533 0 1 2 100 hg38.150200.bed.split10533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10534 0 1 2 100 hg38.150200.bed.split10534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10535 0 1 2 100 hg38.150200.bed.split10535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10536 0 1 2 100 hg38.150200.bed.split10536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10537 0 1 2 100 hg38.150200.bed.split10537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10538 0 1 2 100 hg38.150200.bed.split10538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10539 0 1 2 100 hg38.150200.bed.split10539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1054 0 1 2 100 hg38.150200.bed.split1054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10540 0 1 2 100 hg38.150200.bed.split10540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10541 0 1 2 100 hg38.150200.bed.split10541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10542 0 1 2 100 hg38.150200.bed.split10542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10543 0 1 2 100 hg38.150200.bed.split10543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10544 0 1 2 100 hg38.150200.bed.split10544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10545 0 1 2 100 hg38.150200.bed.split10545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10546 0 1 2 100 hg38.150200.bed.split10546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10547 0 1 2 100 hg38.150200.bed.split10547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10548 0 1 2 100 hg38.150200.bed.split10548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10549 0 1 2 100 hg38.150200.bed.split10549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1055 0 1 2 100 hg38.150200.bed.split1055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10550 0 1 2 100 hg38.150200.bed.split10550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10551 0 1 2 100 hg38.150200.bed.split10551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10552 0 1 2 100 hg38.150200.bed.split10552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10553 0 1 2 100 hg38.150200.bed.split10553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10554 0 1 2 100 hg38.150200.bed.split10554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10555 0 1 2 100 hg38.150200.bed.split10555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10556 0 1 2 100 hg38.150200.bed.split10556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10557 0 1 2 100 hg38.150200.bed.split10557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10558 0 1 2 100 hg38.150200.bed.split10558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10559 0 1 2 100 hg38.150200.bed.split10559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1056 0 1 2 100 hg38.150200.bed.split1056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10560 0 1 2 100 hg38.150200.bed.split10560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10561 0 1 2 100 hg38.150200.bed.split10561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10562 0 1 2 100 hg38.150200.bed.split10562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10563 0 1 2 100 hg38.150200.bed.split10563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10564 0 1 2 100 hg38.150200.bed.split10564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10565 0 1 2 100 hg38.150200.bed.split10565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10566 0 1 2 100 hg38.150200.bed.split10566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10567 0 1 2 100 hg38.150200.bed.split10567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10568 0 1 2 100 hg38.150200.bed.split10568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10569 0 1 2 100 hg38.150200.bed.split10569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1057 0 1 2 100 hg38.150200.bed.split1057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10570 0 1 2 100 hg38.150200.bed.split10570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10571 0 1 2 100 hg38.150200.bed.split10571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10572 0 1 2 100 hg38.150200.bed.split10572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10573 0 1 2 100 hg38.150200.bed.split10573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10574 0 1 2 100 hg38.150200.bed.split10574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10575 0 1 2 100 hg38.150200.bed.split10575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10576 0 1 2 100 hg38.150200.bed.split10576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10577 0 1 2 100 hg38.150200.bed.split10577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10578 0 1 2 100 hg38.150200.bed.split10578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10579 0 1 2 100 hg38.150200.bed.split10579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1058 0 1 2 100 hg38.150200.bed.split1058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10580 0 1 2 100 hg38.150200.bed.split10580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10581 0 1 2 100 hg38.150200.bed.split10581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10582 0 1 2 100 hg38.150200.bed.split10582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10583 0 1 2 100 hg38.150200.bed.split10583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10584 0 1 2 100 hg38.150200.bed.split10584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10585 0 1 2 100 hg38.150200.bed.split10585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10586 0 1 2 100 hg38.150200.bed.split10586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10587 0 1 2 100 hg38.150200.bed.split10587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10588 0 1 2 100 hg38.150200.bed.split10588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10589 0 1 2 100 hg38.150200.bed.split10589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1059 0 1 2 100 hg38.150200.bed.split1059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10590 0 1 2 100 hg38.150200.bed.split10590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10591 0 1 2 100 hg38.150200.bed.split10591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10592 0 1 2 100 hg38.150200.bed.split10592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10593 0 1 2 100 hg38.150200.bed.split10593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10594 0 1 2 100 hg38.150200.bed.split10594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10595 0 1 2 100 hg38.150200.bed.split10595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10596 0 1 2 100 hg38.150200.bed.split10596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10597 0 1 2 100 hg38.150200.bed.split10597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10598 0 1 2 100 hg38.150200.bed.split10598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10599 0 1 2 100 hg38.150200.bed.split10599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split106 0 1 2 100 hg38.150200.bed.split106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1060 0 1 2 100 hg38.150200.bed.split1060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10600 0 1 2 100 hg38.150200.bed.split10600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10601 0 1 2 100 hg38.150200.bed.split10601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10602 0 1 2 100 hg38.150200.bed.split10602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10603 0 1 2 100 hg38.150200.bed.split10603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10604 0 1 2 100 hg38.150200.bed.split10604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10605 0 1 2 100 hg38.150200.bed.split10605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10606 0 1 2 100 hg38.150200.bed.split10606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10607 0 1 2 100 hg38.150200.bed.split10607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10608 0 1 2 100 hg38.150200.bed.split10608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10609 0 1 2 100 hg38.150200.bed.split10609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1061 0 1 2 100 hg38.150200.bed.split1061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10610 0 1 2 100 hg38.150200.bed.split10610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10611 0 1 2 100 hg38.150200.bed.split10611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10612 0 1 2 100 hg38.150200.bed.split10612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10613 0 1 2 100 hg38.150200.bed.split10613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10614 0 1 2 100 hg38.150200.bed.split10614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10615 0 1 2 100 hg38.150200.bed.split10615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10616 0 1 2 100 hg38.150200.bed.split10616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10617 0 1 2 100 hg38.150200.bed.split10617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10618 0 1 2 100 hg38.150200.bed.split10618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10619 0 1 2 100 hg38.150200.bed.split10619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1062 0 1 2 100 hg38.150200.bed.split1062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10620 0 1 2 100 hg38.150200.bed.split10620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10621 0 1 2 100 hg38.150200.bed.split10621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10622 0 1 2 100 hg38.150200.bed.split10622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10623 0 1 2 100 hg38.150200.bed.split10623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10624 0 1 2 100 hg38.150200.bed.split10624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10625 0 1 2 100 hg38.150200.bed.split10625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10626 0 1 2 100 hg38.150200.bed.split10626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10627 0 1 2 100 hg38.150200.bed.split10627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10628 0 1 2 100 hg38.150200.bed.split10628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10629 0 1 2 100 hg38.150200.bed.split10629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1063 0 1 2 100 hg38.150200.bed.split1063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10630 0 1 2 100 hg38.150200.bed.split10630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10631 0 1 2 100 hg38.150200.bed.split10631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10632 0 1 2 100 hg38.150200.bed.split10632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10633 0 1 2 100 hg38.150200.bed.split10633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10634 0 1 2 100 hg38.150200.bed.split10634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10635 0 1 2 100 hg38.150200.bed.split10635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10636 0 1 2 100 hg38.150200.bed.split10636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10637 0 1 2 100 hg38.150200.bed.split10637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10638 0 1 2 100 hg38.150200.bed.split10638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10639 0 1 2 100 hg38.150200.bed.split10639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1064 0 1 2 100 hg38.150200.bed.split1064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10640 0 1 2 100 hg38.150200.bed.split10640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10641 0 1 2 100 hg38.150200.bed.split10641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10642 0 1 2 100 hg38.150200.bed.split10642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10643 0 1 2 100 hg38.150200.bed.split10643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10644 0 1 2 100 hg38.150200.bed.split10644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10645 0 1 2 100 hg38.150200.bed.split10645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10646 0 1 2 100 hg38.150200.bed.split10646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10647 0 1 2 100 hg38.150200.bed.split10647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10648 0 1 2 100 hg38.150200.bed.split10648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10649 0 1 2 100 hg38.150200.bed.split10649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1065 0 1 2 100 hg38.150200.bed.split1065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10650 0 1 2 100 hg38.150200.bed.split10650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10651 0 1 2 100 hg38.150200.bed.split10651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10652 0 1 2 100 hg38.150200.bed.split10652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10653 0 1 2 100 hg38.150200.bed.split10653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10654 0 1 2 100 hg38.150200.bed.split10654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10655 0 1 2 100 hg38.150200.bed.split10655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10656 0 1 2 100 hg38.150200.bed.split10656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10657 0 1 2 100 hg38.150200.bed.split10657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10658 0 1 2 100 hg38.150200.bed.split10658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10659 0 1 2 100 hg38.150200.bed.split10659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1066 0 1 2 100 hg38.150200.bed.split1066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10660 0 1 2 100 hg38.150200.bed.split10660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10661 0 1 2 100 hg38.150200.bed.split10661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10662 0 1 2 100 hg38.150200.bed.split10662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10663 0 1 2 100 hg38.150200.bed.split10663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10664 0 1 2 100 hg38.150200.bed.split10664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10665 0 1 2 100 hg38.150200.bed.split10665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10666 0 1 2 100 hg38.150200.bed.split10666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10667 0 1 2 100 hg38.150200.bed.split10667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10668 0 1 2 100 hg38.150200.bed.split10668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10669 0 1 2 100 hg38.150200.bed.split10669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1067 0 1 2 100 hg38.150200.bed.split1067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10670 0 1 2 100 hg38.150200.bed.split10670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10671 0 1 2 100 hg38.150200.bed.split10671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10672 0 1 2 100 hg38.150200.bed.split10672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10673 0 1 2 100 hg38.150200.bed.split10673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10674 0 1 2 100 hg38.150200.bed.split10674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10675 0 1 2 100 hg38.150200.bed.split10675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10676 0 1 2 100 hg38.150200.bed.split10676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10677 0 1 2 100 hg38.150200.bed.split10677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10678 0 1 2 100 hg38.150200.bed.split10678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10679 0 1 2 100 hg38.150200.bed.split10679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1068 0 1 2 100 hg38.150200.bed.split1068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10680 0 1 2 100 hg38.150200.bed.split10680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10681 0 1 2 100 hg38.150200.bed.split10681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10682 0 1 2 100 hg38.150200.bed.split10682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10683 0 1 2 100 hg38.150200.bed.split10683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10684 0 1 2 100 hg38.150200.bed.split10684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10685 0 1 2 100 hg38.150200.bed.split10685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10686 0 1 2 100 hg38.150200.bed.split10686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10687 0 1 2 100 hg38.150200.bed.split10687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10688 0 1 2 100 hg38.150200.bed.split10688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10689 0 1 2 100 hg38.150200.bed.split10689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1069 0 1 2 100 hg38.150200.bed.split1069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10690 0 1 2 100 hg38.150200.bed.split10690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10691 0 1 2 100 hg38.150200.bed.split10691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10692 0 1 2 100 hg38.150200.bed.split10692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10693 0 1 2 100 hg38.150200.bed.split10693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10694 0 1 2 100 hg38.150200.bed.split10694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10695 0 1 2 100 hg38.150200.bed.split10695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10696 0 1 2 100 hg38.150200.bed.split10696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10697 0 1 2 100 hg38.150200.bed.split10697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10698 0 1 2 100 hg38.150200.bed.split10698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10699 0 1 2 100 hg38.150200.bed.split10699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split107 0 1 2 100 hg38.150200.bed.split107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1070 0 1 2 100 hg38.150200.bed.split1070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10700 0 1 2 100 hg38.150200.bed.split10700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10701 0 1 2 100 hg38.150200.bed.split10701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10702 0 1 2 100 hg38.150200.bed.split10702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10703 0 1 2 100 hg38.150200.bed.split10703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10704 0 1 2 100 hg38.150200.bed.split10704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10705 0 1 2 100 hg38.150200.bed.split10705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10706 0 1 2 100 hg38.150200.bed.split10706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10707 0 1 2 100 hg38.150200.bed.split10707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10708 0 1 2 100 hg38.150200.bed.split10708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10709 0 1 2 100 hg38.150200.bed.split10709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1071 0 1 2 100 hg38.150200.bed.split1071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10710 0 1 2 100 hg38.150200.bed.split10710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10711 0 1 2 100 hg38.150200.bed.split10711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10712 0 1 2 100 hg38.150200.bed.split10712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10713 0 1 2 100 hg38.150200.bed.split10713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10714 0 1 2 100 hg38.150200.bed.split10714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10715 0 1 2 100 hg38.150200.bed.split10715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10716 0 1 2 100 hg38.150200.bed.split10716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10717 0 1 2 100 hg38.150200.bed.split10717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10718 0 1 2 100 hg38.150200.bed.split10718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10719 0 1 2 100 hg38.150200.bed.split10719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1072 0 1 2 100 hg38.150200.bed.split1072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10720 0 1 2 100 hg38.150200.bed.split10720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10721 0 1 2 100 hg38.150200.bed.split10721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10722 0 1 2 100 hg38.150200.bed.split10722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10723 0 1 2 100 hg38.150200.bed.split10723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10724 0 1 2 100 hg38.150200.bed.split10724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10725 0 1 2 100 hg38.150200.bed.split10725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10726 0 1 2 100 hg38.150200.bed.split10726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10727 0 1 2 100 hg38.150200.bed.split10727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10728 0 1 2 100 hg38.150200.bed.split10728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10729 0 1 2 100 hg38.150200.bed.split10729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1073 0 1 2 100 hg38.150200.bed.split1073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10730 0 1 2 100 hg38.150200.bed.split10730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10731 0 1 2 100 hg38.150200.bed.split10731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10732 0 1 2 100 hg38.150200.bed.split10732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10733 0 1 2 100 hg38.150200.bed.split10733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10734 0 1 2 100 hg38.150200.bed.split10734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10735 0 1 2 100 hg38.150200.bed.split10735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10736 0 1 2 100 hg38.150200.bed.split10736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10737 0 1 2 100 hg38.150200.bed.split10737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10738 0 1 2 100 hg38.150200.bed.split10738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10739 0 1 2 100 hg38.150200.bed.split10739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1074 0 1 2 100 hg38.150200.bed.split1074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10740 0 1 2 100 hg38.150200.bed.split10740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10741 0 1 2 100 hg38.150200.bed.split10741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10742 0 1 2 100 hg38.150200.bed.split10742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10743 0 1 2 100 hg38.150200.bed.split10743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10744 0 1 2 100 hg38.150200.bed.split10744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10745 0 1 2 100 hg38.150200.bed.split10745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10746 0 1 2 100 hg38.150200.bed.split10746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10747 0 1 2 100 hg38.150200.bed.split10747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10748 0 1 2 100 hg38.150200.bed.split10748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10749 0 1 2 100 hg38.150200.bed.split10749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1075 0 1 2 100 hg38.150200.bed.split1075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10750 0 1 2 100 hg38.150200.bed.split10750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10751 0 1 2 100 hg38.150200.bed.split10751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10752 0 1 2 100 hg38.150200.bed.split10752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10753 0 1 2 100 hg38.150200.bed.split10753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10754 0 1 2 100 hg38.150200.bed.split10754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10755 0 1 2 100 hg38.150200.bed.split10755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10756 0 1 2 100 hg38.150200.bed.split10756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10757 0 1 2 100 hg38.150200.bed.split10757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10758 0 1 2 100 hg38.150200.bed.split10758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10759 0 1 2 100 hg38.150200.bed.split10759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1076 0 1 2 100 hg38.150200.bed.split1076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10760 0 1 2 100 hg38.150200.bed.split10760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10761 0 1 2 100 hg38.150200.bed.split10761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10762 0 1 2 100 hg38.150200.bed.split10762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10763 0 1 2 100 hg38.150200.bed.split10763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10764 0 1 2 100 hg38.150200.bed.split10764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10765 0 1 2 100 hg38.150200.bed.split10765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10766 0 1 2 100 hg38.150200.bed.split10766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10767 0 1 2 100 hg38.150200.bed.split10767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10768 0 1 2 100 hg38.150200.bed.split10768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10769 0 1 2 100 hg38.150200.bed.split10769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1077 0 1 2 100 hg38.150200.bed.split1077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10770 0 1 2 100 hg38.150200.bed.split10770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10771 0 1 2 100 hg38.150200.bed.split10771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10772 0 1 2 100 hg38.150200.bed.split10772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10773 0 1 2 100 hg38.150200.bed.split10773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10774 0 1 2 100 hg38.150200.bed.split10774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10775 0 1 2 100 hg38.150200.bed.split10775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10776 0 1 2 100 hg38.150200.bed.split10776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10777 0 1 2 100 hg38.150200.bed.split10777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10778 0 1 2 100 hg38.150200.bed.split10778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10779 0 1 2 100 hg38.150200.bed.split10779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1078 0 1 2 100 hg38.150200.bed.split1078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10780 0 1 2 100 hg38.150200.bed.split10780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10781 0 1 2 100 hg38.150200.bed.split10781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10782 0 1 2 100 hg38.150200.bed.split10782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10783 0 1 2 100 hg38.150200.bed.split10783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10784 0 1 2 100 hg38.150200.bed.split10784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10785 0 1 2 100 hg38.150200.bed.split10785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10786 0 1 2 100 hg38.150200.bed.split10786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10787 0 1 2 100 hg38.150200.bed.split10787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10788 0 1 2 100 hg38.150200.bed.split10788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10789 0 1 2 100 hg38.150200.bed.split10789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1079 0 1 2 100 hg38.150200.bed.split1079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10790 0 1 2 100 hg38.150200.bed.split10790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10791 0 1 2 100 hg38.150200.bed.split10791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10792 0 1 2 100 hg38.150200.bed.split10792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10793 0 1 2 100 hg38.150200.bed.split10793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10794 0 1 2 100 hg38.150200.bed.split10794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10795 0 1 2 100 hg38.150200.bed.split10795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10796 0 1 2 100 hg38.150200.bed.split10796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10797 0 1 2 100 hg38.150200.bed.split10797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10798 0 1 2 100 hg38.150200.bed.split10798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10799 0 1 2 100 hg38.150200.bed.split10799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split108 0 1 2 100 hg38.150200.bed.split108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1080 0 1 2 100 hg38.150200.bed.split1080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10800 0 1 2 100 hg38.150200.bed.split10800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10801 0 1 2 100 hg38.150200.bed.split10801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10802 0 1 2 100 hg38.150200.bed.split10802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10803 0 1 2 100 hg38.150200.bed.split10803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10804 0 1 2 100 hg38.150200.bed.split10804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10805 0 1 2 100 hg38.150200.bed.split10805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10806 0 1 2 100 hg38.150200.bed.split10806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10807 0 1 2 100 hg38.150200.bed.split10807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10808 0 1 2 100 hg38.150200.bed.split10808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10809 0 1 2 100 hg38.150200.bed.split10809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1081 0 1 2 100 hg38.150200.bed.split1081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10810 0 1 2 100 hg38.150200.bed.split10810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10811 0 1 2 100 hg38.150200.bed.split10811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10812 0 1 2 100 hg38.150200.bed.split10812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10813 0 1 2 100 hg38.150200.bed.split10813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10814 0 1 2 100 hg38.150200.bed.split10814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10815 0 1 2 100 hg38.150200.bed.split10815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10816 0 1 2 100 hg38.150200.bed.split10816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10817 0 1 2 100 hg38.150200.bed.split10817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10818 0 1 2 100 hg38.150200.bed.split10818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10819 0 1 2 100 hg38.150200.bed.split10819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1082 0 1 2 100 hg38.150200.bed.split1082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10820 0 1 2 100 hg38.150200.bed.split10820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10821 0 1 2 100 hg38.150200.bed.split10821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10822 0 1 2 100 hg38.150200.bed.split10822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10823 0 1 2 100 hg38.150200.bed.split10823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10824 0 1 2 100 hg38.150200.bed.split10824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10825 0 1 2 100 hg38.150200.bed.split10825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10826 0 1 2 100 hg38.150200.bed.split10826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10827 0 1 2 100 hg38.150200.bed.split10827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10828 0 1 2 100 hg38.150200.bed.split10828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10829 0 1 2 100 hg38.150200.bed.split10829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1083 0 1 2 100 hg38.150200.bed.split1083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10830 0 1 2 100 hg38.150200.bed.split10830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10831 0 1 2 100 hg38.150200.bed.split10831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10832 0 1 2 100 hg38.150200.bed.split10832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10833 0 1 2 100 hg38.150200.bed.split10833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10834 0 1 2 100 hg38.150200.bed.split10834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10835 0 1 2 100 hg38.150200.bed.split10835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10836 0 1 2 100 hg38.150200.bed.split10836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10837 0 1 2 100 hg38.150200.bed.split10837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10838 0 1 2 100 hg38.150200.bed.split10838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10839 0 1 2 100 hg38.150200.bed.split10839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1084 0 1 2 100 hg38.150200.bed.split1084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10840 0 1 2 100 hg38.150200.bed.split10840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10841 0 1 2 100 hg38.150200.bed.split10841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10842 0 1 2 100 hg38.150200.bed.split10842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10843 0 1 2 100 hg38.150200.bed.split10843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10844 0 1 2 100 hg38.150200.bed.split10844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10845 0 1 2 100 hg38.150200.bed.split10845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10846 0 1 2 100 hg38.150200.bed.split10846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10847 0 1 2 100 hg38.150200.bed.split10847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10848 0 1 2 100 hg38.150200.bed.split10848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10849 0 1 2 100 hg38.150200.bed.split10849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1085 0 1 2 100 hg38.150200.bed.split1085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10850 0 1 2 100 hg38.150200.bed.split10850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10851 0 1 2 100 hg38.150200.bed.split10851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10852 0 1 2 100 hg38.150200.bed.split10852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10853 0 1 2 100 hg38.150200.bed.split10853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10854 0 1 2 100 hg38.150200.bed.split10854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10855 0 1 2 100 hg38.150200.bed.split10855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10856 0 1 2 100 hg38.150200.bed.split10856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10857 0 1 2 100 hg38.150200.bed.split10857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10858 0 1 2 100 hg38.150200.bed.split10858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10859 0 1 2 100 hg38.150200.bed.split10859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1086 0 1 2 100 hg38.150200.bed.split1086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10860 0 1 2 100 hg38.150200.bed.split10860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10861 0 1 2 100 hg38.150200.bed.split10861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10862 0 1 2 100 hg38.150200.bed.split10862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10863 0 1 2 100 hg38.150200.bed.split10863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10864 0 1 2 100 hg38.150200.bed.split10864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10865 0 1 2 100 hg38.150200.bed.split10865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10866 0 1 2 100 hg38.150200.bed.split10866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10867 0 1 2 100 hg38.150200.bed.split10867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10868 0 1 2 100 hg38.150200.bed.split10868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10869 0 1 2 100 hg38.150200.bed.split10869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1087 0 1 2 100 hg38.150200.bed.split1087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10870 0 1 2 100 hg38.150200.bed.split10870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10871 0 1 2 100 hg38.150200.bed.split10871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10872 0 1 2 100 hg38.150200.bed.split10872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10873 0 1 2 100 hg38.150200.bed.split10873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10874 0 1 2 100 hg38.150200.bed.split10874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10875 0 1 2 100 hg38.150200.bed.split10875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10876 0 1 2 100 hg38.150200.bed.split10876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10877 0 1 2 100 hg38.150200.bed.split10877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10878 0 1 2 100 hg38.150200.bed.split10878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10879 0 1 2 100 hg38.150200.bed.split10879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1088 0 1 2 100 hg38.150200.bed.split1088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10880 0 1 2 100 hg38.150200.bed.split10880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10881 0 1 2 100 hg38.150200.bed.split10881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10882 0 1 2 100 hg38.150200.bed.split10882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10883 0 1 2 100 hg38.150200.bed.split10883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10884 0 1 2 100 hg38.150200.bed.split10884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10885 0 1 2 100 hg38.150200.bed.split10885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10886 0 1 2 100 hg38.150200.bed.split10886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10887 0 1 2 100 hg38.150200.bed.split10887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10888 0 1 2 100 hg38.150200.bed.split10888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10889 0 1 2 100 hg38.150200.bed.split10889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1089 0 1 2 100 hg38.150200.bed.split1089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10890 0 1 2 100 hg38.150200.bed.split10890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10891 0 1 2 100 hg38.150200.bed.split10891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10892 0 1 2 100 hg38.150200.bed.split10892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10893 0 1 2 100 hg38.150200.bed.split10893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10894 0 1 2 100 hg38.150200.bed.split10894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10895 0 1 2 100 hg38.150200.bed.split10895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10896 0 1 2 100 hg38.150200.bed.split10896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10897 0 1 2 100 hg38.150200.bed.split10897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10898 0 1 2 100 hg38.150200.bed.split10898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10899 0 1 2 100 hg38.150200.bed.split10899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split109 0 1 2 100 hg38.150200.bed.split109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1090 0 1 2 100 hg38.150200.bed.split1090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10900 0 1 2 100 hg38.150200.bed.split10900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10901 0 1 2 100 hg38.150200.bed.split10901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10902 0 1 2 100 hg38.150200.bed.split10902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10903 0 1 2 100 hg38.150200.bed.split10903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10904 0 1 2 100 hg38.150200.bed.split10904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10905 0 1 2 100 hg38.150200.bed.split10905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10906 0 1 2 100 hg38.150200.bed.split10906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10907 0 1 2 100 hg38.150200.bed.split10907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10908 0 1 2 100 hg38.150200.bed.split10908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10909 0 1 2 100 hg38.150200.bed.split10909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1091 0 1 2 100 hg38.150200.bed.split1091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10910 0 1 2 100 hg38.150200.bed.split10910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10911 0 1 2 100 hg38.150200.bed.split10911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10912 0 1 2 100 hg38.150200.bed.split10912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10913 0 1 2 100 hg38.150200.bed.split10913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10914 0 1 2 100 hg38.150200.bed.split10914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10915 0 1 2 100 hg38.150200.bed.split10915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10916 0 1 2 100 hg38.150200.bed.split10916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10917 0 1 2 100 hg38.150200.bed.split10917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10918 0 1 2 100 hg38.150200.bed.split10918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10919 0 1 2 100 hg38.150200.bed.split10919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1092 0 1 2 100 hg38.150200.bed.split1092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10920 0 1 2 100 hg38.150200.bed.split10920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10921 0 1 2 100 hg38.150200.bed.split10921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10922 0 1 2 100 hg38.150200.bed.split10922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10923 0 1 2 100 hg38.150200.bed.split10923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10924 0 1 2 100 hg38.150200.bed.split10924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10925 0 1 2 100 hg38.150200.bed.split10925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10926 0 1 2 100 hg38.150200.bed.split10926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10927 0 1 2 100 hg38.150200.bed.split10927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10928 0 1 2 100 hg38.150200.bed.split10928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10929 0 1 2 100 hg38.150200.bed.split10929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1093 0 1 2 100 hg38.150200.bed.split1093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10930 0 1 2 100 hg38.150200.bed.split10930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10931 0 1 2 100 hg38.150200.bed.split10931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10932 0 1 2 100 hg38.150200.bed.split10932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10933 0 1 2 100 hg38.150200.bed.split10933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10934 0 1 2 100 hg38.150200.bed.split10934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10935 0 1 2 100 hg38.150200.bed.split10935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10936 0 1 2 100 hg38.150200.bed.split10936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10937 0 1 2 100 hg38.150200.bed.split10937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10938 0 1 2 100 hg38.150200.bed.split10938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10939 0 1 2 100 hg38.150200.bed.split10939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1094 0 1 2 100 hg38.150200.bed.split1094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10940 0 1 2 100 hg38.150200.bed.split10940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10941 0 1 2 100 hg38.150200.bed.split10941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10942 0 1 2 100 hg38.150200.bed.split10942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10943 0 1 2 100 hg38.150200.bed.split10943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10944 0 1 2 100 hg38.150200.bed.split10944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10945 0 1 2 100 hg38.150200.bed.split10945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10946 0 1 2 100 hg38.150200.bed.split10946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10947 0 1 2 100 hg38.150200.bed.split10947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10948 0 1 2 100 hg38.150200.bed.split10948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10949 0 1 2 100 hg38.150200.bed.split10949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1095 0 1 2 100 hg38.150200.bed.split1095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10950 0 1 2 100 hg38.150200.bed.split10950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10951 0 1 2 100 hg38.150200.bed.split10951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10952 0 1 2 100 hg38.150200.bed.split10952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10953 0 1 2 100 hg38.150200.bed.split10953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10954 0 1 2 100 hg38.150200.bed.split10954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10955 0 1 2 100 hg38.150200.bed.split10955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10956 0 1 2 100 hg38.150200.bed.split10956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10957 0 1 2 100 hg38.150200.bed.split10957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10958 0 1 2 100 hg38.150200.bed.split10958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10959 0 1 2 100 hg38.150200.bed.split10959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1096 0 1 2 100 hg38.150200.bed.split1096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10960 0 1 2 100 hg38.150200.bed.split10960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10961 0 1 2 100 hg38.150200.bed.split10961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10962 0 1 2 100 hg38.150200.bed.split10962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10963 0 1 2 100 hg38.150200.bed.split10963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10964 0 1 2 100 hg38.150200.bed.split10964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10965 0 1 2 100 hg38.150200.bed.split10965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10966 0 1 2 100 hg38.150200.bed.split10966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10967 0 1 2 100 hg38.150200.bed.split10967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10968 0 1 2 100 hg38.150200.bed.split10968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10969 0 1 2 100 hg38.150200.bed.split10969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1097 0 1 2 100 hg38.150200.bed.split1097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10970 0 1 2 100 hg38.150200.bed.split10970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10971 0 1 2 100 hg38.150200.bed.split10971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10972 0 1 2 100 hg38.150200.bed.split10972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10973 0 1 2 100 hg38.150200.bed.split10973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10974 0 1 2 100 hg38.150200.bed.split10974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10975 0 1 2 100 hg38.150200.bed.split10975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10976 0 1 2 100 hg38.150200.bed.split10976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10977 0 1 2 100 hg38.150200.bed.split10977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10978 0 1 2 100 hg38.150200.bed.split10978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10979 0 1 2 100 hg38.150200.bed.split10979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1098 0 1 2 100 hg38.150200.bed.split1098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10980 0 1 2 100 hg38.150200.bed.split10980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10981 0 1 2 100 hg38.150200.bed.split10981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10982 0 1 2 100 hg38.150200.bed.split10982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10983 0 1 2 100 hg38.150200.bed.split10983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10984 0 1 2 100 hg38.150200.bed.split10984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10985 0 1 2 100 hg38.150200.bed.split10985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10986 0 1 2 100 hg38.150200.bed.split10986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10987 0 1 2 100 hg38.150200.bed.split10987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10988 0 1 2 100 hg38.150200.bed.split10988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10989 0 1 2 100 hg38.150200.bed.split10989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1099 0 1 2 100 hg38.150200.bed.split1099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10990 0 1 2 100 hg38.150200.bed.split10990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10991 0 1 2 100 hg38.150200.bed.split10991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10992 0 1 2 100 hg38.150200.bed.split10992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10993 0 1 2 100 hg38.150200.bed.split10993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10994 0 1 2 100 hg38.150200.bed.split10994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10995 0 1 2 100 hg38.150200.bed.split10995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10996 0 1 2 100 hg38.150200.bed.split10996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10997 0 1 2 100 hg38.150200.bed.split10997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10998 0 1 2 100 hg38.150200.bed.split10998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split10999 0 1 2 100 hg38.150200.bed.split10999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11 0 1 2 100 hg38.150200.bed.split11.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split110 0 1 2 100 hg38.150200.bed.split110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1100 0 1 2 100 hg38.150200.bed.split1100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11000 0 1 2 100 hg38.150200.bed.split11000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11001 0 1 2 100 hg38.150200.bed.split11001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11002 0 1 2 100 hg38.150200.bed.split11002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11003 0 1 2 100 hg38.150200.bed.split11003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11004 0 1 2 100 hg38.150200.bed.split11004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11005 0 1 2 100 hg38.150200.bed.split11005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11006 0 1 2 100 hg38.150200.bed.split11006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11007 0 1 2 100 hg38.150200.bed.split11007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11008 0 1 2 100 hg38.150200.bed.split11008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11009 0 1 2 100 hg38.150200.bed.split11009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1101 0 1 2 100 hg38.150200.bed.split1101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11010 0 1 2 100 hg38.150200.bed.split11010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11011 0 1 2 100 hg38.150200.bed.split11011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11012 0 1 2 100 hg38.150200.bed.split11012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11013 0 1 2 100 hg38.150200.bed.split11013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11014 0 1 2 100 hg38.150200.bed.split11014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11015 0 1 2 100 hg38.150200.bed.split11015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11016 0 1 2 100 hg38.150200.bed.split11016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11017 0 1 2 100 hg38.150200.bed.split11017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11018 0 1 2 100 hg38.150200.bed.split11018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11019 0 1 2 100 hg38.150200.bed.split11019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1102 0 1 2 100 hg38.150200.bed.split1102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11020 0 1 2 100 hg38.150200.bed.split11020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11021 0 1 2 100 hg38.150200.bed.split11021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11022 0 1 2 100 hg38.150200.bed.split11022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11023 0 1 2 100 hg38.150200.bed.split11023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11024 0 1 2 100 hg38.150200.bed.split11024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11025 0 1 2 100 hg38.150200.bed.split11025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11026 0 1 2 100 hg38.150200.bed.split11026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11027 0 1 2 100 hg38.150200.bed.split11027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11028 0 1 2 100 hg38.150200.bed.split11028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11029 0 1 2 100 hg38.150200.bed.split11029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1103 0 1 2 100 hg38.150200.bed.split1103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11030 0 1 2 100 hg38.150200.bed.split11030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11031 0 1 2 100 hg38.150200.bed.split11031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11032 0 1 2 100 hg38.150200.bed.split11032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11033 0 1 2 100 hg38.150200.bed.split11033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11034 0 1 2 100 hg38.150200.bed.split11034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11035 0 1 2 100 hg38.150200.bed.split11035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11036 0 1 2 100 hg38.150200.bed.split11036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11037 0 1 2 100 hg38.150200.bed.split11037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11038 0 1 2 100 hg38.150200.bed.split11038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11039 0 1 2 100 hg38.150200.bed.split11039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1104 0 1 2 100 hg38.150200.bed.split1104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11040 0 1 2 100 hg38.150200.bed.split11040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11041 0 1 2 100 hg38.150200.bed.split11041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11042 0 1 2 100 hg38.150200.bed.split11042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11043 0 1 2 100 hg38.150200.bed.split11043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11044 0 1 2 100 hg38.150200.bed.split11044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11045 0 1 2 100 hg38.150200.bed.split11045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11046 0 1 2 100 hg38.150200.bed.split11046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11047 0 1 2 100 hg38.150200.bed.split11047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11048 0 1 2 100 hg38.150200.bed.split11048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11049 0 1 2 100 hg38.150200.bed.split11049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1105 0 1 2 100 hg38.150200.bed.split1105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11050 0 1 2 100 hg38.150200.bed.split11050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11051 0 1 2 100 hg38.150200.bed.split11051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11052 0 1 2 100 hg38.150200.bed.split11052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11053 0 1 2 100 hg38.150200.bed.split11053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11054 0 1 2 100 hg38.150200.bed.split11054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11055 0 1 2 100 hg38.150200.bed.split11055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11056 0 1 2 100 hg38.150200.bed.split11056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11057 0 1 2 100 hg38.150200.bed.split11057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11058 0 1 2 100 hg38.150200.bed.split11058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11059 0 1 2 100 hg38.150200.bed.split11059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1106 0 1 2 100 hg38.150200.bed.split1106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11060 0 1 2 100 hg38.150200.bed.split11060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11061 0 1 2 100 hg38.150200.bed.split11061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11062 0 1 2 100 hg38.150200.bed.split11062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11063 0 1 2 100 hg38.150200.bed.split11063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11064 0 1 2 100 hg38.150200.bed.split11064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11065 0 1 2 100 hg38.150200.bed.split11065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11066 0 1 2 100 hg38.150200.bed.split11066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11067 0 1 2 100 hg38.150200.bed.split11067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11068 0 1 2 100 hg38.150200.bed.split11068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11069 0 1 2 100 hg38.150200.bed.split11069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1107 0 1 2 100 hg38.150200.bed.split1107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11070 0 1 2 100 hg38.150200.bed.split11070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11071 0 1 2 100 hg38.150200.bed.split11071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11072 0 1 2 100 hg38.150200.bed.split11072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11073 0 1 2 100 hg38.150200.bed.split11073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11074 0 1 2 100 hg38.150200.bed.split11074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11075 0 1 2 100 hg38.150200.bed.split11075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11076 0 1 2 100 hg38.150200.bed.split11076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11077 0 1 2 100 hg38.150200.bed.split11077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11078 0 1 2 100 hg38.150200.bed.split11078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11079 0 1 2 100 hg38.150200.bed.split11079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1108 0 1 2 100 hg38.150200.bed.split1108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11080 0 1 2 100 hg38.150200.bed.split11080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11081 0 1 2 100 hg38.150200.bed.split11081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11082 0 1 2 100 hg38.150200.bed.split11082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11083 0 1 2 100 hg38.150200.bed.split11083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11084 0 1 2 100 hg38.150200.bed.split11084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11085 0 1 2 100 hg38.150200.bed.split11085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11086 0 1 2 100 hg38.150200.bed.split11086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11087 0 1 2 100 hg38.150200.bed.split11087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11088 0 1 2 100 hg38.150200.bed.split11088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11089 0 1 2 100 hg38.150200.bed.split11089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1109 0 1 2 100 hg38.150200.bed.split1109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11090 0 1 2 100 hg38.150200.bed.split11090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11091 0 1 2 100 hg38.150200.bed.split11091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11092 0 1 2 100 hg38.150200.bed.split11092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11093 0 1 2 100 hg38.150200.bed.split11093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11094 0 1 2 100 hg38.150200.bed.split11094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11095 0 1 2 100 hg38.150200.bed.split11095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11096 0 1 2 100 hg38.150200.bed.split11096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11097 0 1 2 100 hg38.150200.bed.split11097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11098 0 1 2 100 hg38.150200.bed.split11098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11099 0 1 2 100 hg38.150200.bed.split11099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split111 0 1 2 100 hg38.150200.bed.split111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1110 0 1 2 100 hg38.150200.bed.split1110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11100 0 1 2 100 hg38.150200.bed.split11100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11101 0 1 2 100 hg38.150200.bed.split11101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11102 0 1 2 100 hg38.150200.bed.split11102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11103 0 1 2 100 hg38.150200.bed.split11103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11104 0 1 2 100 hg38.150200.bed.split11104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11105 0 1 2 100 hg38.150200.bed.split11105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11106 0 1 2 100 hg38.150200.bed.split11106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11107 0 1 2 100 hg38.150200.bed.split11107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11108 0 1 2 100 hg38.150200.bed.split11108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11109 0 1 2 100 hg38.150200.bed.split11109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1111 0 1 2 100 hg38.150200.bed.split1111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11110 0 1 2 100 hg38.150200.bed.split11110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11111 0 1 2 100 hg38.150200.bed.split11111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11112 0 1 2 100 hg38.150200.bed.split11112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11113 0 1 2 100 hg38.150200.bed.split11113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11114 0 1 2 100 hg38.150200.bed.split11114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11115 0 1 2 100 hg38.150200.bed.split11115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11116 0 1 2 100 hg38.150200.bed.split11116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11117 0 1 2 100 hg38.150200.bed.split11117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11118 0 1 2 100 hg38.150200.bed.split11118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11119 0 1 2 100 hg38.150200.bed.split11119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1112 0 1 2 100 hg38.150200.bed.split1112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11120 0 1 2 100 hg38.150200.bed.split11120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11121 0 1 2 100 hg38.150200.bed.split11121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11122 0 1 2 100 hg38.150200.bed.split11122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11123 0 1 2 100 hg38.150200.bed.split11123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11124 0 1 2 100 hg38.150200.bed.split11124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11125 0 1 2 100 hg38.150200.bed.split11125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11126 0 1 2 100 hg38.150200.bed.split11126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11127 0 1 2 100 hg38.150200.bed.split11127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11128 0 1 2 100 hg38.150200.bed.split11128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11129 0 1 2 100 hg38.150200.bed.split11129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1113 0 1 2 100 hg38.150200.bed.split1113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11130 0 1 2 100 hg38.150200.bed.split11130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11131 0 1 2 100 hg38.150200.bed.split11131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11132 0 1 2 100 hg38.150200.bed.split11132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11133 0 1 2 100 hg38.150200.bed.split11133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11134 0 1 2 100 hg38.150200.bed.split11134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11135 0 1 2 100 hg38.150200.bed.split11135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11136 0 1 2 100 hg38.150200.bed.split11136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11137 0 1 2 100 hg38.150200.bed.split11137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11138 0 1 2 100 hg38.150200.bed.split11138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11139 0 1 2 100 hg38.150200.bed.split11139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1114 0 1 2 100 hg38.150200.bed.split1114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11140 0 1 2 100 hg38.150200.bed.split11140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11141 0 1 2 100 hg38.150200.bed.split11141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11142 0 1 2 100 hg38.150200.bed.split11142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11143 0 1 2 100 hg38.150200.bed.split11143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11144 0 1 2 100 hg38.150200.bed.split11144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11145 0 1 2 100 hg38.150200.bed.split11145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11146 0 1 2 100 hg38.150200.bed.split11146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11147 0 1 2 100 hg38.150200.bed.split11147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11148 0 1 2 100 hg38.150200.bed.split11148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11149 0 1 2 100 hg38.150200.bed.split11149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1115 0 1 2 100 hg38.150200.bed.split1115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11150 0 1 2 100 hg38.150200.bed.split11150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11151 0 1 2 100 hg38.150200.bed.split11151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11152 0 1 2 100 hg38.150200.bed.split11152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11153 0 1 2 100 hg38.150200.bed.split11153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11154 0 1 2 100 hg38.150200.bed.split11154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11155 0 1 2 100 hg38.150200.bed.split11155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11156 0 1 2 100 hg38.150200.bed.split11156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11157 0 1 2 100 hg38.150200.bed.split11157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11158 0 1 2 100 hg38.150200.bed.split11158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11159 0 1 2 100 hg38.150200.bed.split11159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1116 0 1 2 100 hg38.150200.bed.split1116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11160 0 1 2 100 hg38.150200.bed.split11160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11161 0 1 2 100 hg38.150200.bed.split11161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11162 0 1 2 100 hg38.150200.bed.split11162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11163 0 1 2 100 hg38.150200.bed.split11163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11164 0 1 2 100 hg38.150200.bed.split11164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11165 0 1 2 100 hg38.150200.bed.split11165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11166 0 1 2 100 hg38.150200.bed.split11166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11167 0 1 2 100 hg38.150200.bed.split11167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11168 0 1 2 100 hg38.150200.bed.split11168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11169 0 1 2 100 hg38.150200.bed.split11169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1117 0 1 2 100 hg38.150200.bed.split1117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11170 0 1 2 100 hg38.150200.bed.split11170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11171 0 1 2 100 hg38.150200.bed.split11171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11172 0 1 2 100 hg38.150200.bed.split11172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11173 0 1 2 100 hg38.150200.bed.split11173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11174 0 1 2 100 hg38.150200.bed.split11174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11175 0 1 2 100 hg38.150200.bed.split11175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11176 0 1 2 100 hg38.150200.bed.split11176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11177 0 1 2 100 hg38.150200.bed.split11177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11178 0 1 2 100 hg38.150200.bed.split11178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11179 0 1 2 100 hg38.150200.bed.split11179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1118 0 1 2 100 hg38.150200.bed.split1118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11180 0 1 2 100 hg38.150200.bed.split11180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11181 0 1 2 100 hg38.150200.bed.split11181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11182 0 1 2 100 hg38.150200.bed.split11182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11183 0 1 2 100 hg38.150200.bed.split11183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11184 0 1 2 100 hg38.150200.bed.split11184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11185 0 1 2 100 hg38.150200.bed.split11185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11186 0 1 2 100 hg38.150200.bed.split11186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11187 0 1 2 100 hg38.150200.bed.split11187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11188 0 1 2 100 hg38.150200.bed.split11188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11189 0 1 2 100 hg38.150200.bed.split11189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1119 0 1 2 100 hg38.150200.bed.split1119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11190 0 1 2 100 hg38.150200.bed.split11190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11191 0 1 2 100 hg38.150200.bed.split11191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11192 0 1 2 100 hg38.150200.bed.split11192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11193 0 1 2 100 hg38.150200.bed.split11193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11194 0 1 2 100 hg38.150200.bed.split11194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11195 0 1 2 100 hg38.150200.bed.split11195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11196 0 1 2 100 hg38.150200.bed.split11196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11197 0 1 2 100 hg38.150200.bed.split11197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11198 0 1 2 100 hg38.150200.bed.split11198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11199 0 1 2 100 hg38.150200.bed.split11199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split112 0 1 2 100 hg38.150200.bed.split112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1120 0 1 2 100 hg38.150200.bed.split1120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11200 0 1 2 100 hg38.150200.bed.split11200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11201 0 1 2 100 hg38.150200.bed.split11201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11202 0 1 2 100 hg38.150200.bed.split11202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11203 0 1 2 100 hg38.150200.bed.split11203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11204 0 1 2 100 hg38.150200.bed.split11204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11205 0 1 2 100 hg38.150200.bed.split11205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11206 0 1 2 100 hg38.150200.bed.split11206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11207 0 1 2 100 hg38.150200.bed.split11207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11208 0 1 2 100 hg38.150200.bed.split11208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11209 0 1 2 100 hg38.150200.bed.split11209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1121 0 1 2 100 hg38.150200.bed.split1121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11210 0 1 2 100 hg38.150200.bed.split11210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11211 0 1 2 100 hg38.150200.bed.split11211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11212 0 1 2 100 hg38.150200.bed.split11212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11213 0 1 2 100 hg38.150200.bed.split11213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11214 0 1 2 100 hg38.150200.bed.split11214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11215 0 1 2 100 hg38.150200.bed.split11215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11216 0 1 2 100 hg38.150200.bed.split11216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11217 0 1 2 100 hg38.150200.bed.split11217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11218 0 1 2 100 hg38.150200.bed.split11218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11219 0 1 2 100 hg38.150200.bed.split11219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1122 0 1 2 100 hg38.150200.bed.split1122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11220 0 1 2 100 hg38.150200.bed.split11220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11221 0 1 2 100 hg38.150200.bed.split11221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11222 0 1 2 100 hg38.150200.bed.split11222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11223 0 1 2 100 hg38.150200.bed.split11223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11224 0 1 2 100 hg38.150200.bed.split11224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11225 0 1 2 100 hg38.150200.bed.split11225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11226 0 1 2 100 hg38.150200.bed.split11226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11227 0 1 2 100 hg38.150200.bed.split11227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11228 0 1 2 100 hg38.150200.bed.split11228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11229 0 1 2 100 hg38.150200.bed.split11229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1123 0 1 2 100 hg38.150200.bed.split1123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11230 0 1 2 100 hg38.150200.bed.split11230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11231 0 1 2 100 hg38.150200.bed.split11231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11232 0 1 2 100 hg38.150200.bed.split11232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11233 0 1 2 100 hg38.150200.bed.split11233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11234 0 1 2 100 hg38.150200.bed.split11234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11235 0 1 2 100 hg38.150200.bed.split11235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11236 0 1 2 100 hg38.150200.bed.split11236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11237 0 1 2 100 hg38.150200.bed.split11237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11238 0 1 2 100 hg38.150200.bed.split11238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11239 0 1 2 100 hg38.150200.bed.split11239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1124 0 1 2 100 hg38.150200.bed.split1124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11240 0 1 2 100 hg38.150200.bed.split11240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11241 0 1 2 100 hg38.150200.bed.split11241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11242 0 1 2 100 hg38.150200.bed.split11242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11243 0 1 2 100 hg38.150200.bed.split11243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11244 0 1 2 100 hg38.150200.bed.split11244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11245 0 1 2 100 hg38.150200.bed.split11245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11246 0 1 2 100 hg38.150200.bed.split11246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11247 0 1 2 100 hg38.150200.bed.split11247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11248 0 1 2 100 hg38.150200.bed.split11248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11249 0 1 2 100 hg38.150200.bed.split11249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1125 0 1 2 100 hg38.150200.bed.split1125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11250 0 1 2 100 hg38.150200.bed.split11250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11251 0 1 2 100 hg38.150200.bed.split11251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11252 0 1 2 100 hg38.150200.bed.split11252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11253 0 1 2 100 hg38.150200.bed.split11253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11254 0 1 2 100 hg38.150200.bed.split11254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11255 0 1 2 100 hg38.150200.bed.split11255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11256 0 1 2 100 hg38.150200.bed.split11256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11257 0 1 2 100 hg38.150200.bed.split11257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11258 0 1 2 100 hg38.150200.bed.split11258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11259 0 1 2 100 hg38.150200.bed.split11259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1126 0 1 2 100 hg38.150200.bed.split1126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11260 0 1 2 100 hg38.150200.bed.split11260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11261 0 1 2 100 hg38.150200.bed.split11261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11262 0 1 2 100 hg38.150200.bed.split11262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11263 0 1 2 100 hg38.150200.bed.split11263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11264 0 1 2 100 hg38.150200.bed.split11264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11265 0 1 2 100 hg38.150200.bed.split11265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11266 0 1 2 100 hg38.150200.bed.split11266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11267 0 1 2 100 hg38.150200.bed.split11267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11268 0 1 2 100 hg38.150200.bed.split11268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11269 0 1 2 100 hg38.150200.bed.split11269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1127 0 1 2 100 hg38.150200.bed.split1127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11270 0 1 2 100 hg38.150200.bed.split11270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11271 0 1 2 100 hg38.150200.bed.split11271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11272 0 1 2 100 hg38.150200.bed.split11272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11273 0 1 2 100 hg38.150200.bed.split11273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11274 0 1 2 100 hg38.150200.bed.split11274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11275 0 1 2 100 hg38.150200.bed.split11275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11276 0 1 2 100 hg38.150200.bed.split11276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11277 0 1 2 100 hg38.150200.bed.split11277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11278 0 1 2 100 hg38.150200.bed.split11278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11279 0 1 2 100 hg38.150200.bed.split11279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1128 0 1 2 100 hg38.150200.bed.split1128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11280 0 1 2 100 hg38.150200.bed.split11280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11281 0 1 2 100 hg38.150200.bed.split11281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11282 0 1 2 100 hg38.150200.bed.split11282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11283 0 1 2 100 hg38.150200.bed.split11283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11284 0 1 2 100 hg38.150200.bed.split11284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11285 0 1 2 100 hg38.150200.bed.split11285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11286 0 1 2 100 hg38.150200.bed.split11286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11287 0 1 2 100 hg38.150200.bed.split11287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11288 0 1 2 100 hg38.150200.bed.split11288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11289 0 1 2 100 hg38.150200.bed.split11289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1129 0 1 2 100 hg38.150200.bed.split1129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11290 0 1 2 100 hg38.150200.bed.split11290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11291 0 1 2 100 hg38.150200.bed.split11291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11292 0 1 2 100 hg38.150200.bed.split11292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11293 0 1 2 100 hg38.150200.bed.split11293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11294 0 1 2 100 hg38.150200.bed.split11294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11295 0 1 2 100 hg38.150200.bed.split11295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11296 0 1 2 100 hg38.150200.bed.split11296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11297 0 1 2 100 hg38.150200.bed.split11297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11298 0 1 2 100 hg38.150200.bed.split11298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11299 0 1 2 100 hg38.150200.bed.split11299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split113 0 1 2 100 hg38.150200.bed.split113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1130 0 1 2 100 hg38.150200.bed.split1130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11300 0 1 2 100 hg38.150200.bed.split11300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11301 0 1 2 100 hg38.150200.bed.split11301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11302 0 1 2 100 hg38.150200.bed.split11302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11303 0 1 2 100 hg38.150200.bed.split11303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11304 0 1 2 100 hg38.150200.bed.split11304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11305 0 1 2 100 hg38.150200.bed.split11305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11306 0 1 2 100 hg38.150200.bed.split11306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11307 0 1 2 100 hg38.150200.bed.split11307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11308 0 1 2 100 hg38.150200.bed.split11308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11309 0 1 2 100 hg38.150200.bed.split11309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1131 0 1 2 100 hg38.150200.bed.split1131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11310 0 1 2 100 hg38.150200.bed.split11310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11311 0 1 2 100 hg38.150200.bed.split11311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11312 0 1 2 100 hg38.150200.bed.split11312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11313 0 1 2 100 hg38.150200.bed.split11313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11314 0 1 2 100 hg38.150200.bed.split11314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11315 0 1 2 100 hg38.150200.bed.split11315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11316 0 1 2 100 hg38.150200.bed.split11316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11317 0 1 2 100 hg38.150200.bed.split11317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11318 0 1 2 100 hg38.150200.bed.split11318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11319 0 1 2 100 hg38.150200.bed.split11319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1132 0 1 2 100 hg38.150200.bed.split1132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11320 0 1 2 100 hg38.150200.bed.split11320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11321 0 1 2 100 hg38.150200.bed.split11321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11322 0 1 2 100 hg38.150200.bed.split11322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11323 0 1 2 100 hg38.150200.bed.split11323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11324 0 1 2 100 hg38.150200.bed.split11324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11325 0 1 2 100 hg38.150200.bed.split11325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11326 0 1 2 100 hg38.150200.bed.split11326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11327 0 1 2 100 hg38.150200.bed.split11327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11328 0 1 2 100 hg38.150200.bed.split11328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11329 0 1 2 100 hg38.150200.bed.split11329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1133 0 1 2 100 hg38.150200.bed.split1133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11330 0 1 2 100 hg38.150200.bed.split11330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11331 0 1 2 100 hg38.150200.bed.split11331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11332 0 1 2 100 hg38.150200.bed.split11332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11333 0 1 2 100 hg38.150200.bed.split11333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11334 0 1 2 100 hg38.150200.bed.split11334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11335 0 1 2 100 hg38.150200.bed.split11335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11336 0 1 2 100 hg38.150200.bed.split11336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11337 0 1 2 100 hg38.150200.bed.split11337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11338 0 1 2 100 hg38.150200.bed.split11338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11339 0 1 2 100 hg38.150200.bed.split11339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1134 0 1 2 100 hg38.150200.bed.split1134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11340 0 1 2 100 hg38.150200.bed.split11340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11341 0 1 2 100 hg38.150200.bed.split11341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11342 0 1 2 100 hg38.150200.bed.split11342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11343 0 1 2 100 hg38.150200.bed.split11343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11344 0 1 2 100 hg38.150200.bed.split11344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11345 0 1 2 100 hg38.150200.bed.split11345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11346 0 1 2 100 hg38.150200.bed.split11346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11347 0 1 2 100 hg38.150200.bed.split11347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11348 0 1 2 100 hg38.150200.bed.split11348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11349 0 1 2 100 hg38.150200.bed.split11349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1135 0 1 2 100 hg38.150200.bed.split1135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11350 0 1 2 100 hg38.150200.bed.split11350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11351 0 1 2 100 hg38.150200.bed.split11351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11352 0 1 2 100 hg38.150200.bed.split11352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11353 0 1 2 100 hg38.150200.bed.split11353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11354 0 1 2 100 hg38.150200.bed.split11354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11355 0 1 2 100 hg38.150200.bed.split11355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11356 0 1 2 100 hg38.150200.bed.split11356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11357 0 1 2 100 hg38.150200.bed.split11357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11358 0 1 2 100 hg38.150200.bed.split11358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11359 0 1 2 100 hg38.150200.bed.split11359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1136 0 1 2 100 hg38.150200.bed.split1136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11360 0 1 2 100 hg38.150200.bed.split11360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11361 0 1 2 100 hg38.150200.bed.split11361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11362 0 1 2 100 hg38.150200.bed.split11362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11363 0 1 2 100 hg38.150200.bed.split11363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11364 0 1 2 100 hg38.150200.bed.split11364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11365 0 1 2 100 hg38.150200.bed.split11365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11366 0 1 2 100 hg38.150200.bed.split11366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11367 0 1 2 100 hg38.150200.bed.split11367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11368 0 1 2 100 hg38.150200.bed.split11368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11369 0 1 2 100 hg38.150200.bed.split11369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1137 0 1 2 100 hg38.150200.bed.split1137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11370 0 1 2 100 hg38.150200.bed.split11370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11371 0 1 2 100 hg38.150200.bed.split11371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11372 0 1 2 100 hg38.150200.bed.split11372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11373 0 1 2 100 hg38.150200.bed.split11373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11374 0 1 2 100 hg38.150200.bed.split11374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11375 0 1 2 100 hg38.150200.bed.split11375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11376 0 1 2 100 hg38.150200.bed.split11376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11377 0 1 2 100 hg38.150200.bed.split11377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11378 0 1 2 100 hg38.150200.bed.split11378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11379 0 1 2 100 hg38.150200.bed.split11379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1138 0 1 2 100 hg38.150200.bed.split1138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11380 0 1 2 100 hg38.150200.bed.split11380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11381 0 1 2 100 hg38.150200.bed.split11381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11382 0 1 2 100 hg38.150200.bed.split11382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11383 0 1 2 100 hg38.150200.bed.split11383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11384 0 1 2 100 hg38.150200.bed.split11384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11385 0 1 2 100 hg38.150200.bed.split11385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11386 0 1 2 100 hg38.150200.bed.split11386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11387 0 1 2 100 hg38.150200.bed.split11387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11388 0 1 2 100 hg38.150200.bed.split11388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11389 0 1 2 100 hg38.150200.bed.split11389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1139 0 1 2 100 hg38.150200.bed.split1139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11390 0 1 2 100 hg38.150200.bed.split11390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11391 0 1 2 100 hg38.150200.bed.split11391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11392 0 1 2 100 hg38.150200.bed.split11392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11393 0 1 2 100 hg38.150200.bed.split11393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11394 0 1 2 100 hg38.150200.bed.split11394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11395 0 1 2 100 hg38.150200.bed.split11395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11396 0 1 2 100 hg38.150200.bed.split11396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11397 0 1 2 100 hg38.150200.bed.split11397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11398 0 1 2 100 hg38.150200.bed.split11398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11399 0 1 2 100 hg38.150200.bed.split11399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split114 0 1 2 100 hg38.150200.bed.split114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1140 0 1 2 100 hg38.150200.bed.split1140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11400 0 1 2 100 hg38.150200.bed.split11400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11401 0 1 2 100 hg38.150200.bed.split11401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11402 0 1 2 100 hg38.150200.bed.split11402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11403 0 1 2 100 hg38.150200.bed.split11403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11404 0 1 2 100 hg38.150200.bed.split11404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11405 0 1 2 100 hg38.150200.bed.split11405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11406 0 1 2 100 hg38.150200.bed.split11406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11407 0 1 2 100 hg38.150200.bed.split11407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11408 0 1 2 100 hg38.150200.bed.split11408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11409 0 1 2 100 hg38.150200.bed.split11409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1141 0 1 2 100 hg38.150200.bed.split1141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11410 0 1 2 100 hg38.150200.bed.split11410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11411 0 1 2 100 hg38.150200.bed.split11411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11412 0 1 2 100 hg38.150200.bed.split11412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11413 0 1 2 100 hg38.150200.bed.split11413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11414 0 1 2 100 hg38.150200.bed.split11414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11415 0 1 2 100 hg38.150200.bed.split11415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11416 0 1 2 100 hg38.150200.bed.split11416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11417 0 1 2 100 hg38.150200.bed.split11417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11418 0 1 2 100 hg38.150200.bed.split11418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11419 0 1 2 100 hg38.150200.bed.split11419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1142 0 1 2 100 hg38.150200.bed.split1142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11420 0 1 2 100 hg38.150200.bed.split11420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11421 0 1 2 100 hg38.150200.bed.split11421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11422 0 1 2 100 hg38.150200.bed.split11422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11423 0 1 2 100 hg38.150200.bed.split11423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11424 0 1 2 100 hg38.150200.bed.split11424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11425 0 1 2 100 hg38.150200.bed.split11425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11426 0 1 2 100 hg38.150200.bed.split11426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11427 0 1 2 100 hg38.150200.bed.split11427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11428 0 1 2 100 hg38.150200.bed.split11428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11429 0 1 2 100 hg38.150200.bed.split11429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1143 0 1 2 100 hg38.150200.bed.split1143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11430 0 1 2 100 hg38.150200.bed.split11430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11431 0 1 2 100 hg38.150200.bed.split11431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11432 0 1 2 100 hg38.150200.bed.split11432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11433 0 1 2 100 hg38.150200.bed.split11433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11434 0 1 2 100 hg38.150200.bed.split11434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11435 0 1 2 100 hg38.150200.bed.split11435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11436 0 1 2 100 hg38.150200.bed.split11436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11437 0 1 2 100 hg38.150200.bed.split11437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11438 0 1 2 100 hg38.150200.bed.split11438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11439 0 1 2 100 hg38.150200.bed.split11439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1144 0 1 2 100 hg38.150200.bed.split1144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11440 0 1 2 100 hg38.150200.bed.split11440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11441 0 1 2 100 hg38.150200.bed.split11441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11442 0 1 2 100 hg38.150200.bed.split11442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11443 0 1 2 100 hg38.150200.bed.split11443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11444 0 1 2 100 hg38.150200.bed.split11444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11445 0 1 2 100 hg38.150200.bed.split11445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11446 0 1 2 100 hg38.150200.bed.split11446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11447 0 1 2 100 hg38.150200.bed.split11447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11448 0 1 2 100 hg38.150200.bed.split11448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11449 0 1 2 100 hg38.150200.bed.split11449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1145 0 1 2 100 hg38.150200.bed.split1145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11450 0 1 2 100 hg38.150200.bed.split11450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11451 0 1 2 100 hg38.150200.bed.split11451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11452 0 1 2 100 hg38.150200.bed.split11452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11453 0 1 2 100 hg38.150200.bed.split11453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11454 0 1 2 100 hg38.150200.bed.split11454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11455 0 1 2 100 hg38.150200.bed.split11455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11456 0 1 2 100 hg38.150200.bed.split11456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11457 0 1 2 100 hg38.150200.bed.split11457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11458 0 1 2 100 hg38.150200.bed.split11458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11459 0 1 2 100 hg38.150200.bed.split11459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1146 0 1 2 100 hg38.150200.bed.split1146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11460 0 1 2 100 hg38.150200.bed.split11460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11461 0 1 2 100 hg38.150200.bed.split11461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11462 0 1 2 100 hg38.150200.bed.split11462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11463 0 1 2 100 hg38.150200.bed.split11463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11464 0 1 2 100 hg38.150200.bed.split11464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11465 0 1 2 100 hg38.150200.bed.split11465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11466 0 1 2 100 hg38.150200.bed.split11466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11467 0 1 2 100 hg38.150200.bed.split11467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11468 0 1 2 100 hg38.150200.bed.split11468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11469 0 1 2 100 hg38.150200.bed.split11469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1147 0 1 2 100 hg38.150200.bed.split1147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11470 0 1 2 100 hg38.150200.bed.split11470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11471 0 1 2 100 hg38.150200.bed.split11471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11472 0 1 2 100 hg38.150200.bed.split11472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11473 0 1 2 100 hg38.150200.bed.split11473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11474 0 1 2 100 hg38.150200.bed.split11474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11475 0 1 2 100 hg38.150200.bed.split11475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11476 0 1 2 100 hg38.150200.bed.split11476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11477 0 1 2 100 hg38.150200.bed.split11477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11478 0 1 2 100 hg38.150200.bed.split11478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11479 0 1 2 100 hg38.150200.bed.split11479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1148 0 1 2 100 hg38.150200.bed.split1148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11480 0 1 2 100 hg38.150200.bed.split11480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11481 0 1 2 100 hg38.150200.bed.split11481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11482 0 1 2 100 hg38.150200.bed.split11482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11483 0 1 2 100 hg38.150200.bed.split11483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11484 0 1 2 100 hg38.150200.bed.split11484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11485 0 1 2 100 hg38.150200.bed.split11485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11486 0 1 2 100 hg38.150200.bed.split11486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11487 0 1 2 100 hg38.150200.bed.split11487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11488 0 1 2 100 hg38.150200.bed.split11488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11489 0 1 2 100 hg38.150200.bed.split11489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1149 0 1 2 100 hg38.150200.bed.split1149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11490 0 1 2 100 hg38.150200.bed.split11490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11491 0 1 2 100 hg38.150200.bed.split11491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11492 0 1 2 100 hg38.150200.bed.split11492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11493 0 1 2 100 hg38.150200.bed.split11493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11494 0 1 2 100 hg38.150200.bed.split11494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11495 0 1 2 100 hg38.150200.bed.split11495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11496 0 1 2 100 hg38.150200.bed.split11496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11497 0 1 2 100 hg38.150200.bed.split11497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11498 0 1 2 100 hg38.150200.bed.split11498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11499 0 1 2 100 hg38.150200.bed.split11499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split115 0 1 2 100 hg38.150200.bed.split115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1150 0 1 2 100 hg38.150200.bed.split1150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11500 0 1 2 100 hg38.150200.bed.split11500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11501 0 1 2 100 hg38.150200.bed.split11501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11502 0 1 2 100 hg38.150200.bed.split11502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11503 0 1 2 100 hg38.150200.bed.split11503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11504 0 1 2 100 hg38.150200.bed.split11504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11505 0 1 2 100 hg38.150200.bed.split11505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11506 0 1 2 100 hg38.150200.bed.split11506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11507 0 1 2 100 hg38.150200.bed.split11507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11508 0 1 2 100 hg38.150200.bed.split11508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11509 0 1 2 100 hg38.150200.bed.split11509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1151 0 1 2 100 hg38.150200.bed.split1151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11510 0 1 2 100 hg38.150200.bed.split11510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11511 0 1 2 100 hg38.150200.bed.split11511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11512 0 1 2 100 hg38.150200.bed.split11512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11513 0 1 2 100 hg38.150200.bed.split11513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11514 0 1 2 100 hg38.150200.bed.split11514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11515 0 1 2 100 hg38.150200.bed.split11515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11516 0 1 2 100 hg38.150200.bed.split11516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11517 0 1 2 100 hg38.150200.bed.split11517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11518 0 1 2 100 hg38.150200.bed.split11518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11519 0 1 2 100 hg38.150200.bed.split11519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1152 0 1 2 100 hg38.150200.bed.split1152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11520 0 1 2 100 hg38.150200.bed.split11520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11521 0 1 2 100 hg38.150200.bed.split11521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11522 0 1 2 100 hg38.150200.bed.split11522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11523 0 1 2 100 hg38.150200.bed.split11523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11524 0 1 2 100 hg38.150200.bed.split11524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11525 0 1 2 100 hg38.150200.bed.split11525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11526 0 1 2 100 hg38.150200.bed.split11526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11527 0 1 2 100 hg38.150200.bed.split11527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11528 0 1 2 100 hg38.150200.bed.split11528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11529 0 1 2 100 hg38.150200.bed.split11529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1153 0 1 2 100 hg38.150200.bed.split1153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11530 0 1 2 100 hg38.150200.bed.split11530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11531 0 1 2 100 hg38.150200.bed.split11531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11532 0 1 2 100 hg38.150200.bed.split11532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11533 0 1 2 100 hg38.150200.bed.split11533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11534 0 1 2 100 hg38.150200.bed.split11534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11535 0 1 2 100 hg38.150200.bed.split11535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11536 0 1 2 100 hg38.150200.bed.split11536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11537 0 1 2 100 hg38.150200.bed.split11537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11538 0 1 2 100 hg38.150200.bed.split11538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11539 0 1 2 100 hg38.150200.bed.split11539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1154 0 1 2 100 hg38.150200.bed.split1154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11540 0 1 2 100 hg38.150200.bed.split11540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11541 0 1 2 100 hg38.150200.bed.split11541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11542 0 1 2 100 hg38.150200.bed.split11542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11543 0 1 2 100 hg38.150200.bed.split11543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11544 0 1 2 100 hg38.150200.bed.split11544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11545 0 1 2 100 hg38.150200.bed.split11545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11546 0 1 2 100 hg38.150200.bed.split11546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11547 0 1 2 100 hg38.150200.bed.split11547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11548 0 1 2 100 hg38.150200.bed.split11548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11549 0 1 2 100 hg38.150200.bed.split11549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1155 0 1 2 100 hg38.150200.bed.split1155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11550 0 1 2 100 hg38.150200.bed.split11550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11551 0 1 2 100 hg38.150200.bed.split11551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11552 0 1 2 100 hg38.150200.bed.split11552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11553 0 1 2 100 hg38.150200.bed.split11553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11554 0 1 2 100 hg38.150200.bed.split11554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11555 0 1 2 100 hg38.150200.bed.split11555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11556 0 1 2 100 hg38.150200.bed.split11556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11557 0 1 2 100 hg38.150200.bed.split11557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11558 0 1 2 100 hg38.150200.bed.split11558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11559 0 1 2 100 hg38.150200.bed.split11559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1156 0 1 2 100 hg38.150200.bed.split1156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11560 0 1 2 100 hg38.150200.bed.split11560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11561 0 1 2 100 hg38.150200.bed.split11561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11562 0 1 2 100 hg38.150200.bed.split11562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11563 0 1 2 100 hg38.150200.bed.split11563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11564 0 1 2 100 hg38.150200.bed.split11564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11565 0 1 2 100 hg38.150200.bed.split11565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11566 0 1 2 100 hg38.150200.bed.split11566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11567 0 1 2 100 hg38.150200.bed.split11567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11568 0 1 2 100 hg38.150200.bed.split11568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11569 0 1 2 100 hg38.150200.bed.split11569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1157 0 1 2 100 hg38.150200.bed.split1157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11570 0 1 2 100 hg38.150200.bed.split11570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11571 0 1 2 100 hg38.150200.bed.split11571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11572 0 1 2 100 hg38.150200.bed.split11572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11573 0 1 2 100 hg38.150200.bed.split11573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11574 0 1 2 100 hg38.150200.bed.split11574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11575 0 1 2 100 hg38.150200.bed.split11575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11576 0 1 2 100 hg38.150200.bed.split11576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11577 0 1 2 100 hg38.150200.bed.split11577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11578 0 1 2 100 hg38.150200.bed.split11578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11579 0 1 2 100 hg38.150200.bed.split11579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1158 0 1 2 100 hg38.150200.bed.split1158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11580 0 1 2 100 hg38.150200.bed.split11580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11581 0 1 2 100 hg38.150200.bed.split11581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11582 0 1 2 100 hg38.150200.bed.split11582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11583 0 1 2 100 hg38.150200.bed.split11583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11584 0 1 2 100 hg38.150200.bed.split11584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11585 0 1 2 100 hg38.150200.bed.split11585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11586 0 1 2 100 hg38.150200.bed.split11586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11587 0 1 2 100 hg38.150200.bed.split11587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11588 0 1 2 100 hg38.150200.bed.split11588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11589 0 1 2 100 hg38.150200.bed.split11589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1159 0 1 2 100 hg38.150200.bed.split1159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11590 0 1 2 100 hg38.150200.bed.split11590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11591 0 1 2 100 hg38.150200.bed.split11591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11592 0 1 2 100 hg38.150200.bed.split11592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11593 0 1 2 100 hg38.150200.bed.split11593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11594 0 1 2 100 hg38.150200.bed.split11594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11595 0 1 2 100 hg38.150200.bed.split11595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11596 0 1 2 100 hg38.150200.bed.split11596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11597 0 1 2 100 hg38.150200.bed.split11597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11598 0 1 2 100 hg38.150200.bed.split11598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11599 0 1 2 100 hg38.150200.bed.split11599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split116 0 1 2 100 hg38.150200.bed.split116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1160 0 1 2 100 hg38.150200.bed.split1160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11600 0 1 2 100 hg38.150200.bed.split11600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11601 0 1 2 100 hg38.150200.bed.split11601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11602 0 1 2 100 hg38.150200.bed.split11602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11603 0 1 2 100 hg38.150200.bed.split11603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11604 0 1 2 100 hg38.150200.bed.split11604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11605 0 1 2 100 hg38.150200.bed.split11605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11606 0 1 2 100 hg38.150200.bed.split11606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11607 0 1 2 100 hg38.150200.bed.split11607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11608 0 1 2 100 hg38.150200.bed.split11608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11609 0 1 2 100 hg38.150200.bed.split11609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1161 0 1 2 100 hg38.150200.bed.split1161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11610 0 1 2 100 hg38.150200.bed.split11610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11611 0 1 2 100 hg38.150200.bed.split11611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11612 0 1 2 100 hg38.150200.bed.split11612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11613 0 1 2 100 hg38.150200.bed.split11613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11614 0 1 2 100 hg38.150200.bed.split11614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11615 0 1 2 100 hg38.150200.bed.split11615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11616 0 1 2 100 hg38.150200.bed.split11616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11617 0 1 2 100 hg38.150200.bed.split11617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11618 0 1 2 100 hg38.150200.bed.split11618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11619 0 1 2 100 hg38.150200.bed.split11619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1162 0 1 2 100 hg38.150200.bed.split1162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11620 0 1 2 100 hg38.150200.bed.split11620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11621 0 1 2 100 hg38.150200.bed.split11621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11622 0 1 2 100 hg38.150200.bed.split11622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11623 0 1 2 100 hg38.150200.bed.split11623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11624 0 1 2 100 hg38.150200.bed.split11624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11625 0 1 2 100 hg38.150200.bed.split11625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11626 0 1 2 100 hg38.150200.bed.split11626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11627 0 1 2 100 hg38.150200.bed.split11627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11628 0 1 2 100 hg38.150200.bed.split11628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11629 0 1 2 100 hg38.150200.bed.split11629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1163 0 1 2 100 hg38.150200.bed.split1163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11630 0 1 2 100 hg38.150200.bed.split11630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11631 0 1 2 100 hg38.150200.bed.split11631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11632 0 1 2 100 hg38.150200.bed.split11632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11633 0 1 2 100 hg38.150200.bed.split11633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11634 0 1 2 100 hg38.150200.bed.split11634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11635 0 1 2 100 hg38.150200.bed.split11635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11636 0 1 2 100 hg38.150200.bed.split11636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11637 0 1 2 100 hg38.150200.bed.split11637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11638 0 1 2 100 hg38.150200.bed.split11638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11639 0 1 2 100 hg38.150200.bed.split11639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1164 0 1 2 100 hg38.150200.bed.split1164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11640 0 1 2 100 hg38.150200.bed.split11640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11641 0 1 2 100 hg38.150200.bed.split11641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11642 0 1 2 100 hg38.150200.bed.split11642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11643 0 1 2 100 hg38.150200.bed.split11643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11644 0 1 2 100 hg38.150200.bed.split11644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11645 0 1 2 100 hg38.150200.bed.split11645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11646 0 1 2 100 hg38.150200.bed.split11646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11647 0 1 2 100 hg38.150200.bed.split11647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11648 0 1 2 100 hg38.150200.bed.split11648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11649 0 1 2 100 hg38.150200.bed.split11649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1165 0 1 2 100 hg38.150200.bed.split1165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11650 0 1 2 100 hg38.150200.bed.split11650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11651 0 1 2 100 hg38.150200.bed.split11651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11652 0 1 2 100 hg38.150200.bed.split11652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11653 0 1 2 100 hg38.150200.bed.split11653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11654 0 1 2 100 hg38.150200.bed.split11654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11655 0 1 2 100 hg38.150200.bed.split11655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11656 0 1 2 100 hg38.150200.bed.split11656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11657 0 1 2 100 hg38.150200.bed.split11657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11658 0 1 2 100 hg38.150200.bed.split11658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11659 0 1 2 100 hg38.150200.bed.split11659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1166 0 1 2 100 hg38.150200.bed.split1166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11660 0 1 2 100 hg38.150200.bed.split11660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11661 0 1 2 100 hg38.150200.bed.split11661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11662 0 1 2 100 hg38.150200.bed.split11662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11663 0 1 2 100 hg38.150200.bed.split11663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11664 0 1 2 100 hg38.150200.bed.split11664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11665 0 1 2 100 hg38.150200.bed.split11665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11666 0 1 2 100 hg38.150200.bed.split11666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11667 0 1 2 100 hg38.150200.bed.split11667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11668 0 1 2 100 hg38.150200.bed.split11668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11669 0 1 2 100 hg38.150200.bed.split11669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1167 0 1 2 100 hg38.150200.bed.split1167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11670 0 1 2 100 hg38.150200.bed.split11670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11671 0 1 2 100 hg38.150200.bed.split11671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11672 0 1 2 100 hg38.150200.bed.split11672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11673 0 1 2 100 hg38.150200.bed.split11673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11674 0 1 2 100 hg38.150200.bed.split11674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11675 0 1 2 100 hg38.150200.bed.split11675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11676 0 1 2 100 hg38.150200.bed.split11676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11677 0 1 2 100 hg38.150200.bed.split11677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11678 0 1 2 100 hg38.150200.bed.split11678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11679 0 1 2 100 hg38.150200.bed.split11679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1168 0 1 2 100 hg38.150200.bed.split1168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11680 0 1 2 100 hg38.150200.bed.split11680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11681 0 1 2 100 hg38.150200.bed.split11681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11682 0 1 2 100 hg38.150200.bed.split11682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11683 0 1 2 100 hg38.150200.bed.split11683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11684 0 1 2 100 hg38.150200.bed.split11684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11685 0 1 2 100 hg38.150200.bed.split11685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11686 0 1 2 100 hg38.150200.bed.split11686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11687 0 1 2 100 hg38.150200.bed.split11687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11688 0 1 2 100 hg38.150200.bed.split11688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11689 0 1 2 100 hg38.150200.bed.split11689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1169 0 1 2 100 hg38.150200.bed.split1169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11690 0 1 2 100 hg38.150200.bed.split11690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11691 0 1 2 100 hg38.150200.bed.split11691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11692 0 1 2 100 hg38.150200.bed.split11692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11693 0 1 2 100 hg38.150200.bed.split11693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11694 0 1 2 100 hg38.150200.bed.split11694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11695 0 1 2 100 hg38.150200.bed.split11695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11696 0 1 2 100 hg38.150200.bed.split11696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11697 0 1 2 100 hg38.150200.bed.split11697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11698 0 1 2 100 hg38.150200.bed.split11698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11699 0 1 2 100 hg38.150200.bed.split11699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split117 0 1 2 100 hg38.150200.bed.split117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1170 0 1 2 100 hg38.150200.bed.split1170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11700 0 1 2 100 hg38.150200.bed.split11700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11701 0 1 2 100 hg38.150200.bed.split11701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11702 0 1 2 100 hg38.150200.bed.split11702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11703 0 1 2 100 hg38.150200.bed.split11703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11704 0 1 2 100 hg38.150200.bed.split11704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11705 0 1 2 100 hg38.150200.bed.split11705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11706 0 1 2 100 hg38.150200.bed.split11706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11707 0 1 2 100 hg38.150200.bed.split11707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11708 0 1 2 100 hg38.150200.bed.split11708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11709 0 1 2 100 hg38.150200.bed.split11709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1171 0 1 2 100 hg38.150200.bed.split1171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11710 0 1 2 100 hg38.150200.bed.split11710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11711 0 1 2 100 hg38.150200.bed.split11711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11712 0 1 2 100 hg38.150200.bed.split11712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11713 0 1 2 100 hg38.150200.bed.split11713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11714 0 1 2 100 hg38.150200.bed.split11714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11715 0 1 2 100 hg38.150200.bed.split11715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11716 0 1 2 100 hg38.150200.bed.split11716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11717 0 1 2 100 hg38.150200.bed.split11717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11718 0 1 2 100 hg38.150200.bed.split11718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11719 0 1 2 100 hg38.150200.bed.split11719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1172 0 1 2 100 hg38.150200.bed.split1172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11720 0 1 2 100 hg38.150200.bed.split11720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11721 0 1 2 100 hg38.150200.bed.split11721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11722 0 1 2 100 hg38.150200.bed.split11722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11723 0 1 2 100 hg38.150200.bed.split11723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11724 0 1 2 100 hg38.150200.bed.split11724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11725 0 1 2 100 hg38.150200.bed.split11725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11726 0 1 2 100 hg38.150200.bed.split11726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11727 0 1 2 100 hg38.150200.bed.split11727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11728 0 1 2 100 hg38.150200.bed.split11728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11729 0 1 2 100 hg38.150200.bed.split11729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1173 0 1 2 100 hg38.150200.bed.split1173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11730 0 1 2 100 hg38.150200.bed.split11730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11731 0 1 2 100 hg38.150200.bed.split11731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11732 0 1 2 100 hg38.150200.bed.split11732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11733 0 1 2 100 hg38.150200.bed.split11733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11734 0 1 2 100 hg38.150200.bed.split11734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11735 0 1 2 100 hg38.150200.bed.split11735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11736 0 1 2 100 hg38.150200.bed.split11736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11737 0 1 2 100 hg38.150200.bed.split11737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11738 0 1 2 100 hg38.150200.bed.split11738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11739 0 1 2 100 hg38.150200.bed.split11739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1174 0 1 2 100 hg38.150200.bed.split1174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11740 0 1 2 100 hg38.150200.bed.split11740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11741 0 1 2 100 hg38.150200.bed.split11741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11742 0 1 2 100 hg38.150200.bed.split11742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11743 0 1 2 100 hg38.150200.bed.split11743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11744 0 1 2 100 hg38.150200.bed.split11744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11745 0 1 2 100 hg38.150200.bed.split11745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11746 0 1 2 100 hg38.150200.bed.split11746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11747 0 1 2 100 hg38.150200.bed.split11747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11748 0 1 2 100 hg38.150200.bed.split11748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11749 0 1 2 100 hg38.150200.bed.split11749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1175 0 1 2 100 hg38.150200.bed.split1175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11750 0 1 2 100 hg38.150200.bed.split11750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11751 0 1 2 100 hg38.150200.bed.split11751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11752 0 1 2 100 hg38.150200.bed.split11752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11753 0 1 2 100 hg38.150200.bed.split11753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11754 0 1 2 100 hg38.150200.bed.split11754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11755 0 1 2 100 hg38.150200.bed.split11755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11756 0 1 2 100 hg38.150200.bed.split11756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11757 0 1 2 100 hg38.150200.bed.split11757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11758 0 1 2 100 hg38.150200.bed.split11758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11759 0 1 2 100 hg38.150200.bed.split11759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1176 0 1 2 100 hg38.150200.bed.split1176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11760 0 1 2 100 hg38.150200.bed.split11760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11761 0 1 2 100 hg38.150200.bed.split11761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11762 0 1 2 100 hg38.150200.bed.split11762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11763 0 1 2 100 hg38.150200.bed.split11763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11764 0 1 2 100 hg38.150200.bed.split11764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11765 0 1 2 100 hg38.150200.bed.split11765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11766 0 1 2 100 hg38.150200.bed.split11766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11767 0 1 2 100 hg38.150200.bed.split11767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11768 0 1 2 100 hg38.150200.bed.split11768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11769 0 1 2 100 hg38.150200.bed.split11769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1177 0 1 2 100 hg38.150200.bed.split1177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11770 0 1 2 100 hg38.150200.bed.split11770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11771 0 1 2 100 hg38.150200.bed.split11771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11772 0 1 2 100 hg38.150200.bed.split11772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11773 0 1 2 100 hg38.150200.bed.split11773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11774 0 1 2 100 hg38.150200.bed.split11774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11775 0 1 2 100 hg38.150200.bed.split11775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11776 0 1 2 100 hg38.150200.bed.split11776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11777 0 1 2 100 hg38.150200.bed.split11777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11778 0 1 2 100 hg38.150200.bed.split11778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11779 0 1 2 100 hg38.150200.bed.split11779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1178 0 1 2 100 hg38.150200.bed.split1178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11780 0 1 2 100 hg38.150200.bed.split11780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11781 0 1 2 100 hg38.150200.bed.split11781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11782 0 1 2 100 hg38.150200.bed.split11782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11783 0 1 2 100 hg38.150200.bed.split11783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11784 0 1 2 100 hg38.150200.bed.split11784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11785 0 1 2 100 hg38.150200.bed.split11785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11786 0 1 2 100 hg38.150200.bed.split11786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11787 0 1 2 100 hg38.150200.bed.split11787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11788 0 1 2 100 hg38.150200.bed.split11788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11789 0 1 2 100 hg38.150200.bed.split11789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1179 0 1 2 100 hg38.150200.bed.split1179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11790 0 1 2 100 hg38.150200.bed.split11790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11791 0 1 2 100 hg38.150200.bed.split11791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11792 0 1 2 100 hg38.150200.bed.split11792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11793 0 1 2 100 hg38.150200.bed.split11793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11794 0 1 2 100 hg38.150200.bed.split11794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11795 0 1 2 100 hg38.150200.bed.split11795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11796 0 1 2 100 hg38.150200.bed.split11796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11797 0 1 2 100 hg38.150200.bed.split11797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11798 0 1 2 100 hg38.150200.bed.split11798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11799 0 1 2 100 hg38.150200.bed.split11799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split118 0 1 2 100 hg38.150200.bed.split118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1180 0 1 2 100 hg38.150200.bed.split1180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11800 0 1 2 100 hg38.150200.bed.split11800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11801 0 1 2 100 hg38.150200.bed.split11801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11802 0 1 2 100 hg38.150200.bed.split11802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11803 0 1 2 100 hg38.150200.bed.split11803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11804 0 1 2 100 hg38.150200.bed.split11804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11805 0 1 2 100 hg38.150200.bed.split11805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11806 0 1 2 100 hg38.150200.bed.split11806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11807 0 1 2 100 hg38.150200.bed.split11807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11808 0 1 2 100 hg38.150200.bed.split11808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11809 0 1 2 100 hg38.150200.bed.split11809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1181 0 1 2 100 hg38.150200.bed.split1181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11810 0 1 2 100 hg38.150200.bed.split11810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11811 0 1 2 100 hg38.150200.bed.split11811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11812 0 1 2 100 hg38.150200.bed.split11812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11813 0 1 2 100 hg38.150200.bed.split11813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11814 0 1 2 100 hg38.150200.bed.split11814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11815 0 1 2 100 hg38.150200.bed.split11815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11816 0 1 2 100 hg38.150200.bed.split11816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11817 0 1 2 100 hg38.150200.bed.split11817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11818 0 1 2 100 hg38.150200.bed.split11818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11819 0 1 2 100 hg38.150200.bed.split11819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1182 0 1 2 100 hg38.150200.bed.split1182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11820 0 1 2 100 hg38.150200.bed.split11820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11821 0 1 2 100 hg38.150200.bed.split11821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11822 0 1 2 100 hg38.150200.bed.split11822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11823 0 1 2 100 hg38.150200.bed.split11823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11824 0 1 2 100 hg38.150200.bed.split11824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11825 0 1 2 100 hg38.150200.bed.split11825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11826 0 1 2 100 hg38.150200.bed.split11826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11827 0 1 2 100 hg38.150200.bed.split11827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11828 0 1 2 100 hg38.150200.bed.split11828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11829 0 1 2 100 hg38.150200.bed.split11829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1183 0 1 2 100 hg38.150200.bed.split1183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11830 0 1 2 100 hg38.150200.bed.split11830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11831 0 1 2 100 hg38.150200.bed.split11831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11832 0 1 2 100 hg38.150200.bed.split11832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11833 0 1 2 100 hg38.150200.bed.split11833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11834 0 1 2 100 hg38.150200.bed.split11834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11835 0 1 2 100 hg38.150200.bed.split11835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11836 0 1 2 100 hg38.150200.bed.split11836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11837 0 1 2 100 hg38.150200.bed.split11837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11838 0 1 2 100 hg38.150200.bed.split11838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11839 0 1 2 100 hg38.150200.bed.split11839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1184 0 1 2 100 hg38.150200.bed.split1184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11840 0 1 2 100 hg38.150200.bed.split11840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11841 0 1 2 100 hg38.150200.bed.split11841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11842 0 1 2 100 hg38.150200.bed.split11842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11843 0 1 2 100 hg38.150200.bed.split11843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11844 0 1 2 100 hg38.150200.bed.split11844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11845 0 1 2 100 hg38.150200.bed.split11845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11846 0 1 2 100 hg38.150200.bed.split11846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11847 0 1 2 100 hg38.150200.bed.split11847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11848 0 1 2 100 hg38.150200.bed.split11848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11849 0 1 2 100 hg38.150200.bed.split11849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1185 0 1 2 100 hg38.150200.bed.split1185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11850 0 1 2 100 hg38.150200.bed.split11850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11851 0 1 2 100 hg38.150200.bed.split11851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11852 0 1 2 100 hg38.150200.bed.split11852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11853 0 1 2 100 hg38.150200.bed.split11853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11854 0 1 2 100 hg38.150200.bed.split11854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11855 0 1 2 100 hg38.150200.bed.split11855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11856 0 1 2 100 hg38.150200.bed.split11856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11857 0 1 2 100 hg38.150200.bed.split11857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11858 0 1 2 100 hg38.150200.bed.split11858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11859 0 1 2 100 hg38.150200.bed.split11859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1186 0 1 2 100 hg38.150200.bed.split1186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11860 0 1 2 100 hg38.150200.bed.split11860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11861 0 1 2 100 hg38.150200.bed.split11861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11862 0 1 2 100 hg38.150200.bed.split11862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11863 0 1 2 100 hg38.150200.bed.split11863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11864 0 1 2 100 hg38.150200.bed.split11864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11865 0 1 2 100 hg38.150200.bed.split11865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11866 0 1 2 100 hg38.150200.bed.split11866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11867 0 1 2 100 hg38.150200.bed.split11867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11868 0 1 2 100 hg38.150200.bed.split11868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11869 0 1 2 100 hg38.150200.bed.split11869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1187 0 1 2 100 hg38.150200.bed.split1187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11870 0 1 2 100 hg38.150200.bed.split11870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11871 0 1 2 100 hg38.150200.bed.split11871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11872 0 1 2 100 hg38.150200.bed.split11872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11873 0 1 2 100 hg38.150200.bed.split11873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11874 0 1 2 100 hg38.150200.bed.split11874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11875 0 1 2 100 hg38.150200.bed.split11875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11876 0 1 2 100 hg38.150200.bed.split11876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11877 0 1 2 100 hg38.150200.bed.split11877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11878 0 1 2 100 hg38.150200.bed.split11878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11879 0 1 2 100 hg38.150200.bed.split11879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1188 0 1 2 100 hg38.150200.bed.split1188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11880 0 1 2 100 hg38.150200.bed.split11880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11881 0 1 2 100 hg38.150200.bed.split11881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11882 0 1 2 100 hg38.150200.bed.split11882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11883 0 1 2 100 hg38.150200.bed.split11883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11884 0 1 2 100 hg38.150200.bed.split11884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11885 0 1 2 100 hg38.150200.bed.split11885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11886 0 1 2 100 hg38.150200.bed.split11886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11887 0 1 2 100 hg38.150200.bed.split11887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11888 0 1 2 100 hg38.150200.bed.split11888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11889 0 1 2 100 hg38.150200.bed.split11889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1189 0 1 2 100 hg38.150200.bed.split1189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11890 0 1 2 100 hg38.150200.bed.split11890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11891 0 1 2 100 hg38.150200.bed.split11891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11892 0 1 2 100 hg38.150200.bed.split11892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11893 0 1 2 100 hg38.150200.bed.split11893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11894 0 1 2 100 hg38.150200.bed.split11894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11895 0 1 2 100 hg38.150200.bed.split11895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11896 0 1 2 100 hg38.150200.bed.split11896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11897 0 1 2 100 hg38.150200.bed.split11897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11898 0 1 2 100 hg38.150200.bed.split11898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11899 0 1 2 100 hg38.150200.bed.split11899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split119 0 1 2 100 hg38.150200.bed.split119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1190 0 1 2 100 hg38.150200.bed.split1190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11900 0 1 2 100 hg38.150200.bed.split11900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11901 0 1 2 100 hg38.150200.bed.split11901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11902 0 1 2 100 hg38.150200.bed.split11902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11903 0 1 2 100 hg38.150200.bed.split11903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11904 0 1 2 100 hg38.150200.bed.split11904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11905 0 1 2 100 hg38.150200.bed.split11905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11906 0 1 2 100 hg38.150200.bed.split11906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11907 0 1 2 100 hg38.150200.bed.split11907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11908 0 1 2 100 hg38.150200.bed.split11908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11909 0 1 2 100 hg38.150200.bed.split11909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1191 0 1 2 100 hg38.150200.bed.split1191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11910 0 1 2 100 hg38.150200.bed.split11910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11911 0 1 2 100 hg38.150200.bed.split11911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11912 0 1 2 100 hg38.150200.bed.split11912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11913 0 1 2 100 hg38.150200.bed.split11913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11914 0 1 2 100 hg38.150200.bed.split11914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11915 0 1 2 100 hg38.150200.bed.split11915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11916 0 1 2 100 hg38.150200.bed.split11916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11917 0 1 2 100 hg38.150200.bed.split11917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11918 0 1 2 100 hg38.150200.bed.split11918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11919 0 1 2 100 hg38.150200.bed.split11919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1192 0 1 2 100 hg38.150200.bed.split1192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11920 0 1 2 100 hg38.150200.bed.split11920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11921 0 1 2 100 hg38.150200.bed.split11921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11922 0 1 2 100 hg38.150200.bed.split11922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11923 0 1 2 100 hg38.150200.bed.split11923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11924 0 1 2 100 hg38.150200.bed.split11924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11925 0 1 2 100 hg38.150200.bed.split11925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11926 0 1 2 100 hg38.150200.bed.split11926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11927 0 1 2 100 hg38.150200.bed.split11927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11928 0 1 2 100 hg38.150200.bed.split11928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11929 0 1 2 100 hg38.150200.bed.split11929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1193 0 1 2 100 hg38.150200.bed.split1193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11930 0 1 2 100 hg38.150200.bed.split11930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11931 0 1 2 100 hg38.150200.bed.split11931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11932 0 1 2 100 hg38.150200.bed.split11932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11933 0 1 2 100 hg38.150200.bed.split11933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11934 0 1 2 100 hg38.150200.bed.split11934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11935 0 1 2 100 hg38.150200.bed.split11935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11936 0 1 2 100 hg38.150200.bed.split11936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11937 0 1 2 100 hg38.150200.bed.split11937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11938 0 1 2 100 hg38.150200.bed.split11938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11939 0 1 2 100 hg38.150200.bed.split11939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1194 0 1 2 100 hg38.150200.bed.split1194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11940 0 1 2 100 hg38.150200.bed.split11940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11941 0 1 2 100 hg38.150200.bed.split11941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11942 0 1 2 100 hg38.150200.bed.split11942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11943 0 1 2 100 hg38.150200.bed.split11943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11944 0 1 2 100 hg38.150200.bed.split11944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11945 0 1 2 100 hg38.150200.bed.split11945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11946 0 1 2 100 hg38.150200.bed.split11946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11947 0 1 2 100 hg38.150200.bed.split11947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11948 0 1 2 100 hg38.150200.bed.split11948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11949 0 1 2 100 hg38.150200.bed.split11949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1195 0 1 2 100 hg38.150200.bed.split1195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11950 0 1 2 100 hg38.150200.bed.split11950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11951 0 1 2 100 hg38.150200.bed.split11951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11952 0 1 2 100 hg38.150200.bed.split11952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11953 0 1 2 100 hg38.150200.bed.split11953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11954 0 1 2 100 hg38.150200.bed.split11954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11955 0 1 2 100 hg38.150200.bed.split11955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11956 0 1 2 100 hg38.150200.bed.split11956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11957 0 1 2 100 hg38.150200.bed.split11957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11958 0 1 2 100 hg38.150200.bed.split11958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11959 0 1 2 100 hg38.150200.bed.split11959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1196 0 1 2 100 hg38.150200.bed.split1196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11960 0 1 2 100 hg38.150200.bed.split11960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11961 0 1 2 100 hg38.150200.bed.split11961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11962 0 1 2 100 hg38.150200.bed.split11962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11963 0 1 2 100 hg38.150200.bed.split11963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11964 0 1 2 100 hg38.150200.bed.split11964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11965 0 1 2 100 hg38.150200.bed.split11965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11966 0 1 2 100 hg38.150200.bed.split11966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11967 0 1 2 100 hg38.150200.bed.split11967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11968 0 1 2 100 hg38.150200.bed.split11968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11969 0 1 2 100 hg38.150200.bed.split11969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1197 0 1 2 100 hg38.150200.bed.split1197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11970 0 1 2 100 hg38.150200.bed.split11970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11971 0 1 2 100 hg38.150200.bed.split11971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11972 0 1 2 100 hg38.150200.bed.split11972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11973 0 1 2 100 hg38.150200.bed.split11973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11974 0 1 2 100 hg38.150200.bed.split11974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11975 0 1 2 100 hg38.150200.bed.split11975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11976 0 1 2 100 hg38.150200.bed.split11976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11977 0 1 2 100 hg38.150200.bed.split11977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11978 0 1 2 100 hg38.150200.bed.split11978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11979 0 1 2 100 hg38.150200.bed.split11979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1198 0 1 2 100 hg38.150200.bed.split1198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11980 0 1 2 100 hg38.150200.bed.split11980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11981 0 1 2 100 hg38.150200.bed.split11981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11982 0 1 2 100 hg38.150200.bed.split11982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11983 0 1 2 100 hg38.150200.bed.split11983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11984 0 1 2 100 hg38.150200.bed.split11984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11985 0 1 2 100 hg38.150200.bed.split11985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11986 0 1 2 100 hg38.150200.bed.split11986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11987 0 1 2 100 hg38.150200.bed.split11987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11988 0 1 2 100 hg38.150200.bed.split11988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11989 0 1 2 100 hg38.150200.bed.split11989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1199 0 1 2 100 hg38.150200.bed.split1199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11990 0 1 2 100 hg38.150200.bed.split11990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11991 0 1 2 100 hg38.150200.bed.split11991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11992 0 1 2 100 hg38.150200.bed.split11992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11993 0 1 2 100 hg38.150200.bed.split11993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11994 0 1 2 100 hg38.150200.bed.split11994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11995 0 1 2 100 hg38.150200.bed.split11995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11996 0 1 2 100 hg38.150200.bed.split11996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11997 0 1 2 100 hg38.150200.bed.split11997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11998 0 1 2 100 hg38.150200.bed.split11998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split11999 0 1 2 100 hg38.150200.bed.split11999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12 0 1 2 100 hg38.150200.bed.split12.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split120 0 1 2 100 hg38.150200.bed.split120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1200 0 1 2 100 hg38.150200.bed.split1200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12000 0 1 2 100 hg38.150200.bed.split12000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12001 0 1 2 100 hg38.150200.bed.split12001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12002 0 1 2 100 hg38.150200.bed.split12002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12003 0 1 2 100 hg38.150200.bed.split12003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12004 0 1 2 100 hg38.150200.bed.split12004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12005 0 1 2 100 hg38.150200.bed.split12005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12006 0 1 2 100 hg38.150200.bed.split12006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12007 0 1 2 100 hg38.150200.bed.split12007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12008 0 1 2 100 hg38.150200.bed.split12008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12009 0 1 2 100 hg38.150200.bed.split12009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1201 0 1 2 100 hg38.150200.bed.split1201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12010 0 1 2 100 hg38.150200.bed.split12010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12011 0 1 2 100 hg38.150200.bed.split12011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12012 0 1 2 100 hg38.150200.bed.split12012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12013 0 1 2 100 hg38.150200.bed.split12013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12014 0 1 2 100 hg38.150200.bed.split12014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12015 0 1 2 100 hg38.150200.bed.split12015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12016 0 1 2 100 hg38.150200.bed.split12016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12017 0 1 2 100 hg38.150200.bed.split12017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12018 0 1 2 100 hg38.150200.bed.split12018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12019 0 1 2 100 hg38.150200.bed.split12019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1202 0 1 2 100 hg38.150200.bed.split1202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12020 0 1 2 100 hg38.150200.bed.split12020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12021 0 1 2 100 hg38.150200.bed.split12021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12022 0 1 2 100 hg38.150200.bed.split12022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12023 0 1 2 100 hg38.150200.bed.split12023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12024 0 1 2 100 hg38.150200.bed.split12024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12025 0 1 2 100 hg38.150200.bed.split12025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12026 0 1 2 100 hg38.150200.bed.split12026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12027 0 1 2 100 hg38.150200.bed.split12027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12028 0 1 2 100 hg38.150200.bed.split12028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12029 0 1 2 100 hg38.150200.bed.split12029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1203 0 1 2 100 hg38.150200.bed.split1203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12030 0 1 2 100 hg38.150200.bed.split12030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12031 0 1 2 100 hg38.150200.bed.split12031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12032 0 1 2 100 hg38.150200.bed.split12032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12033 0 1 2 100 hg38.150200.bed.split12033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12034 0 1 2 100 hg38.150200.bed.split12034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12035 0 1 2 100 hg38.150200.bed.split12035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12036 0 1 2 100 hg38.150200.bed.split12036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12037 0 1 2 100 hg38.150200.bed.split12037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12038 0 1 2 100 hg38.150200.bed.split12038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12039 0 1 2 100 hg38.150200.bed.split12039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1204 0 1 2 100 hg38.150200.bed.split1204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12040 0 1 2 100 hg38.150200.bed.split12040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12041 0 1 2 100 hg38.150200.bed.split12041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12042 0 1 2 100 hg38.150200.bed.split12042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12043 0 1 2 100 hg38.150200.bed.split12043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12044 0 1 2 100 hg38.150200.bed.split12044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12045 0 1 2 100 hg38.150200.bed.split12045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12046 0 1 2 100 hg38.150200.bed.split12046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12047 0 1 2 100 hg38.150200.bed.split12047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12048 0 1 2 100 hg38.150200.bed.split12048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12049 0 1 2 100 hg38.150200.bed.split12049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1205 0 1 2 100 hg38.150200.bed.split1205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12050 0 1 2 100 hg38.150200.bed.split12050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12051 0 1 2 100 hg38.150200.bed.split12051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12052 0 1 2 100 hg38.150200.bed.split12052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12053 0 1 2 100 hg38.150200.bed.split12053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12054 0 1 2 100 hg38.150200.bed.split12054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12055 0 1 2 100 hg38.150200.bed.split12055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12056 0 1 2 100 hg38.150200.bed.split12056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12057 0 1 2 100 hg38.150200.bed.split12057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12058 0 1 2 100 hg38.150200.bed.split12058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12059 0 1 2 100 hg38.150200.bed.split12059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1206 0 1 2 100 hg38.150200.bed.split1206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12060 0 1 2 100 hg38.150200.bed.split12060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12061 0 1 2 100 hg38.150200.bed.split12061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12062 0 1 2 100 hg38.150200.bed.split12062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12063 0 1 2 100 hg38.150200.bed.split12063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12064 0 1 2 100 hg38.150200.bed.split12064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12065 0 1 2 100 hg38.150200.bed.split12065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12066 0 1 2 100 hg38.150200.bed.split12066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12067 0 1 2 100 hg38.150200.bed.split12067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12068 0 1 2 100 hg38.150200.bed.split12068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12069 0 1 2 100 hg38.150200.bed.split12069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1207 0 1 2 100 hg38.150200.bed.split1207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12070 0 1 2 100 hg38.150200.bed.split12070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12071 0 1 2 100 hg38.150200.bed.split12071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12072 0 1 2 100 hg38.150200.bed.split12072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12073 0 1 2 100 hg38.150200.bed.split12073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12074 0 1 2 100 hg38.150200.bed.split12074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12075 0 1 2 100 hg38.150200.bed.split12075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12076 0 1 2 100 hg38.150200.bed.split12076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12077 0 1 2 100 hg38.150200.bed.split12077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12078 0 1 2 100 hg38.150200.bed.split12078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12079 0 1 2 100 hg38.150200.bed.split12079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1208 0 1 2 100 hg38.150200.bed.split1208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12080 0 1 2 100 hg38.150200.bed.split12080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12081 0 1 2 100 hg38.150200.bed.split12081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12082 0 1 2 100 hg38.150200.bed.split12082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12083 0 1 2 100 hg38.150200.bed.split12083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12084 0 1 2 100 hg38.150200.bed.split12084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12085 0 1 2 100 hg38.150200.bed.split12085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12086 0 1 2 100 hg38.150200.bed.split12086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12087 0 1 2 100 hg38.150200.bed.split12087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12088 0 1 2 100 hg38.150200.bed.split12088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12089 0 1 2 100 hg38.150200.bed.split12089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1209 0 1 2 100 hg38.150200.bed.split1209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12090 0 1 2 100 hg38.150200.bed.split12090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12091 0 1 2 100 hg38.150200.bed.split12091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12092 0 1 2 100 hg38.150200.bed.split12092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12093 0 1 2 100 hg38.150200.bed.split12093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12094 0 1 2 100 hg38.150200.bed.split12094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12095 0 1 2 100 hg38.150200.bed.split12095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12096 0 1 2 100 hg38.150200.bed.split12096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12097 0 1 2 100 hg38.150200.bed.split12097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12098 0 1 2 100 hg38.150200.bed.split12098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12099 0 1 2 100 hg38.150200.bed.split12099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split121 0 1 2 100 hg38.150200.bed.split121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1210 0 1 2 100 hg38.150200.bed.split1210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12100 0 1 2 100 hg38.150200.bed.split12100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12101 0 1 2 100 hg38.150200.bed.split12101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12102 0 1 2 100 hg38.150200.bed.split12102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12103 0 1 2 100 hg38.150200.bed.split12103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12104 0 1 2 100 hg38.150200.bed.split12104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12105 0 1 2 100 hg38.150200.bed.split12105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12106 0 1 2 100 hg38.150200.bed.split12106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12107 0 1 2 100 hg38.150200.bed.split12107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12108 0 1 2 100 hg38.150200.bed.split12108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12109 0 1 2 100 hg38.150200.bed.split12109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1211 0 1 2 100 hg38.150200.bed.split1211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12110 0 1 2 100 hg38.150200.bed.split12110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12111 0 1 2 100 hg38.150200.bed.split12111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12112 0 1 2 100 hg38.150200.bed.split12112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12113 0 1 2 100 hg38.150200.bed.split12113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12114 0 1 2 100 hg38.150200.bed.split12114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12115 0 1 2 100 hg38.150200.bed.split12115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12116 0 1 2 100 hg38.150200.bed.split12116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12117 0 1 2 100 hg38.150200.bed.split12117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12118 0 1 2 100 hg38.150200.bed.split12118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12119 0 1 2 100 hg38.150200.bed.split12119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1212 0 1 2 100 hg38.150200.bed.split1212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12120 0 1 2 100 hg38.150200.bed.split12120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12121 0 1 2 100 hg38.150200.bed.split12121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12122 0 1 2 100 hg38.150200.bed.split12122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12123 0 1 2 100 hg38.150200.bed.split12123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12124 0 1 2 100 hg38.150200.bed.split12124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12125 0 1 2 100 hg38.150200.bed.split12125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12126 0 1 2 100 hg38.150200.bed.split12126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12127 0 1 2 100 hg38.150200.bed.split12127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12128 0 1 2 100 hg38.150200.bed.split12128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12129 0 1 2 100 hg38.150200.bed.split12129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1213 0 1 2 100 hg38.150200.bed.split1213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12130 0 1 2 100 hg38.150200.bed.split12130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12131 0 1 2 100 hg38.150200.bed.split12131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12132 0 1 2 100 hg38.150200.bed.split12132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12133 0 1 2 100 hg38.150200.bed.split12133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12134 0 1 2 100 hg38.150200.bed.split12134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12135 0 1 2 100 hg38.150200.bed.split12135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12136 0 1 2 100 hg38.150200.bed.split12136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12137 0 1 2 100 hg38.150200.bed.split12137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12138 0 1 2 100 hg38.150200.bed.split12138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12139 0 1 2 100 hg38.150200.bed.split12139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1214 0 1 2 100 hg38.150200.bed.split1214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12140 0 1 2 100 hg38.150200.bed.split12140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12141 0 1 2 100 hg38.150200.bed.split12141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12142 0 1 2 100 hg38.150200.bed.split12142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12143 0 1 2 100 hg38.150200.bed.split12143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12144 0 1 2 100 hg38.150200.bed.split12144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12145 0 1 2 100 hg38.150200.bed.split12145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12146 0 1 2 100 hg38.150200.bed.split12146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12147 0 1 2 100 hg38.150200.bed.split12147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12148 0 1 2 100 hg38.150200.bed.split12148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12149 0 1 2 100 hg38.150200.bed.split12149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1215 0 1 2 100 hg38.150200.bed.split1215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12150 0 1 2 100 hg38.150200.bed.split12150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12151 0 1 2 100 hg38.150200.bed.split12151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12152 0 1 2 100 hg38.150200.bed.split12152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12153 0 1 2 100 hg38.150200.bed.split12153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12154 0 1 2 100 hg38.150200.bed.split12154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12155 0 1 2 100 hg38.150200.bed.split12155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12156 0 1 2 100 hg38.150200.bed.split12156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12157 0 1 2 100 hg38.150200.bed.split12157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12158 0 1 2 100 hg38.150200.bed.split12158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12159 0 1 2 100 hg38.150200.bed.split12159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1216 0 1 2 100 hg38.150200.bed.split1216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12160 0 1 2 100 hg38.150200.bed.split12160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12161 0 1 2 100 hg38.150200.bed.split12161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12162 0 1 2 100 hg38.150200.bed.split12162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12163 0 1 2 100 hg38.150200.bed.split12163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12164 0 1 2 100 hg38.150200.bed.split12164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12165 0 1 2 100 hg38.150200.bed.split12165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12166 0 1 2 100 hg38.150200.bed.split12166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12167 0 1 2 100 hg38.150200.bed.split12167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12168 0 1 2 100 hg38.150200.bed.split12168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12169 0 1 2 100 hg38.150200.bed.split12169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1217 0 1 2 100 hg38.150200.bed.split1217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12170 0 1 2 100 hg38.150200.bed.split12170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12171 0 1 2 100 hg38.150200.bed.split12171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12172 0 1 2 100 hg38.150200.bed.split12172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12173 0 1 2 100 hg38.150200.bed.split12173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12174 0 1 2 100 hg38.150200.bed.split12174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12175 0 1 2 100 hg38.150200.bed.split12175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12176 0 1 2 100 hg38.150200.bed.split12176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12177 0 1 2 100 hg38.150200.bed.split12177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12178 0 1 2 100 hg38.150200.bed.split12178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12179 0 1 2 100 hg38.150200.bed.split12179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1218 0 1 2 100 hg38.150200.bed.split1218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12180 0 1 2 100 hg38.150200.bed.split12180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12181 0 1 2 100 hg38.150200.bed.split12181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12182 0 1 2 100 hg38.150200.bed.split12182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12183 0 1 2 100 hg38.150200.bed.split12183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12184 0 1 2 100 hg38.150200.bed.split12184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12185 0 1 2 100 hg38.150200.bed.split12185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12186 0 1 2 100 hg38.150200.bed.split12186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12187 0 1 2 100 hg38.150200.bed.split12187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12188 0 1 2 100 hg38.150200.bed.split12188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12189 0 1 2 100 hg38.150200.bed.split12189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1219 0 1 2 100 hg38.150200.bed.split1219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12190 0 1 2 100 hg38.150200.bed.split12190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12191 0 1 2 100 hg38.150200.bed.split12191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12192 0 1 2 100 hg38.150200.bed.split12192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12193 0 1 2 100 hg38.150200.bed.split12193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12194 0 1 2 100 hg38.150200.bed.split12194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12195 0 1 2 100 hg38.150200.bed.split12195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12196 0 1 2 100 hg38.150200.bed.split12196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12197 0 1 2 100 hg38.150200.bed.split12197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12198 0 1 2 100 hg38.150200.bed.split12198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12199 0 1 2 100 hg38.150200.bed.split12199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split122 0 1 2 100 hg38.150200.bed.split122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1220 0 1 2 100 hg38.150200.bed.split1220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12200 0 1 2 100 hg38.150200.bed.split12200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12201 0 1 2 100 hg38.150200.bed.split12201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12202 0 1 2 100 hg38.150200.bed.split12202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12203 0 1 2 100 hg38.150200.bed.split12203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12204 0 1 2 100 hg38.150200.bed.split12204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12205 0 1 2 100 hg38.150200.bed.split12205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12206 0 1 2 100 hg38.150200.bed.split12206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12207 0 1 2 100 hg38.150200.bed.split12207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12208 0 1 2 100 hg38.150200.bed.split12208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12209 0 1 2 100 hg38.150200.bed.split12209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1221 0 1 2 100 hg38.150200.bed.split1221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12210 0 1 2 100 hg38.150200.bed.split12210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12211 0 1 2 100 hg38.150200.bed.split12211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12212 0 1 2 100 hg38.150200.bed.split12212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12213 0 1 2 100 hg38.150200.bed.split12213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12214 0 1 2 100 hg38.150200.bed.split12214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12215 0 1 2 100 hg38.150200.bed.split12215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12216 0 1 2 100 hg38.150200.bed.split12216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12217 0 1 2 100 hg38.150200.bed.split12217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12218 0 1 2 100 hg38.150200.bed.split12218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12219 0 1 2 100 hg38.150200.bed.split12219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1222 0 1 2 100 hg38.150200.bed.split1222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12220 0 1 2 100 hg38.150200.bed.split12220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12221 0 1 2 100 hg38.150200.bed.split12221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12222 0 1 2 100 hg38.150200.bed.split12222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12223 0 1 2 100 hg38.150200.bed.split12223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12224 0 1 2 100 hg38.150200.bed.split12224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12225 0 1 2 100 hg38.150200.bed.split12225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12226 0 1 2 100 hg38.150200.bed.split12226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12227 0 1 2 100 hg38.150200.bed.split12227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12228 0 1 2 100 hg38.150200.bed.split12228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12229 0 1 2 100 hg38.150200.bed.split12229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1223 0 1 2 100 hg38.150200.bed.split1223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12230 0 1 2 100 hg38.150200.bed.split12230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12231 0 1 2 100 hg38.150200.bed.split12231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12232 0 1 2 100 hg38.150200.bed.split12232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12233 0 1 2 100 hg38.150200.bed.split12233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12234 0 1 2 100 hg38.150200.bed.split12234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12235 0 1 2 100 hg38.150200.bed.split12235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12236 0 1 2 100 hg38.150200.bed.split12236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12237 0 1 2 100 hg38.150200.bed.split12237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12238 0 1 2 100 hg38.150200.bed.split12238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12239 0 1 2 100 hg38.150200.bed.split12239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1224 0 1 2 100 hg38.150200.bed.split1224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12240 0 1 2 100 hg38.150200.bed.split12240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12241 0 1 2 100 hg38.150200.bed.split12241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12242 0 1 2 100 hg38.150200.bed.split12242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12243 0 1 2 100 hg38.150200.bed.split12243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12244 0 1 2 100 hg38.150200.bed.split12244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12245 0 1 2 100 hg38.150200.bed.split12245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12246 0 1 2 100 hg38.150200.bed.split12246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12247 0 1 2 100 hg38.150200.bed.split12247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12248 0 1 2 100 hg38.150200.bed.split12248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12249 0 1 2 100 hg38.150200.bed.split12249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1225 0 1 2 100 hg38.150200.bed.split1225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12250 0 1 2 100 hg38.150200.bed.split12250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12251 0 1 2 100 hg38.150200.bed.split12251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12252 0 1 2 100 hg38.150200.bed.split12252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12253 0 1 2 100 hg38.150200.bed.split12253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12254 0 1 2 100 hg38.150200.bed.split12254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12255 0 1 2 100 hg38.150200.bed.split12255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12256 0 1 2 100 hg38.150200.bed.split12256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12257 0 1 2 100 hg38.150200.bed.split12257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12258 0 1 2 100 hg38.150200.bed.split12258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12259 0 1 2 100 hg38.150200.bed.split12259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1226 0 1 2 100 hg38.150200.bed.split1226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12260 0 1 2 100 hg38.150200.bed.split12260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12261 0 1 2 100 hg38.150200.bed.split12261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12262 0 1 2 100 hg38.150200.bed.split12262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12263 0 1 2 100 hg38.150200.bed.split12263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12264 0 1 2 100 hg38.150200.bed.split12264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12265 0 1 2 100 hg38.150200.bed.split12265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12266 0 1 2 100 hg38.150200.bed.split12266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12267 0 1 2 100 hg38.150200.bed.split12267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12268 0 1 2 100 hg38.150200.bed.split12268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12269 0 1 2 100 hg38.150200.bed.split12269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1227 0 1 2 100 hg38.150200.bed.split1227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12270 0 1 2 100 hg38.150200.bed.split12270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12271 0 1 2 100 hg38.150200.bed.split12271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12272 0 1 2 100 hg38.150200.bed.split12272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12273 0 1 2 100 hg38.150200.bed.split12273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12274 0 1 2 100 hg38.150200.bed.split12274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12275 0 1 2 100 hg38.150200.bed.split12275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12276 0 1 2 100 hg38.150200.bed.split12276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12277 0 1 2 100 hg38.150200.bed.split12277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12278 0 1 2 100 hg38.150200.bed.split12278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12279 0 1 2 100 hg38.150200.bed.split12279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1228 0 1 2 100 hg38.150200.bed.split1228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12280 0 1 2 100 hg38.150200.bed.split12280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12281 0 1 2 100 hg38.150200.bed.split12281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12282 0 1 2 100 hg38.150200.bed.split12282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12283 0 1 2 100 hg38.150200.bed.split12283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12284 0 1 2 100 hg38.150200.bed.split12284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12285 0 1 2 100 hg38.150200.bed.split12285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12286 0 1 2 100 hg38.150200.bed.split12286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12287 0 1 2 100 hg38.150200.bed.split12287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12288 0 1 2 100 hg38.150200.bed.split12288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12289 0 1 2 100 hg38.150200.bed.split12289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1229 0 1 2 100 hg38.150200.bed.split1229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12290 0 1 2 100 hg38.150200.bed.split12290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12291 0 1 2 100 hg38.150200.bed.split12291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12292 0 1 2 100 hg38.150200.bed.split12292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12293 0 1 2 100 hg38.150200.bed.split12293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12294 0 1 2 100 hg38.150200.bed.split12294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12295 0 1 2 100 hg38.150200.bed.split12295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12296 0 1 2 100 hg38.150200.bed.split12296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12297 0 1 2 100 hg38.150200.bed.split12297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12298 0 1 2 100 hg38.150200.bed.split12298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12299 0 1 2 100 hg38.150200.bed.split12299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split123 0 1 2 100 hg38.150200.bed.split123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1230 0 1 2 100 hg38.150200.bed.split1230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12300 0 1 2 100 hg38.150200.bed.split12300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12301 0 1 2 100 hg38.150200.bed.split12301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12302 0 1 2 100 hg38.150200.bed.split12302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12303 0 1 2 100 hg38.150200.bed.split12303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12304 0 1 2 100 hg38.150200.bed.split12304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12305 0 1 2 100 hg38.150200.bed.split12305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12306 0 1 2 100 hg38.150200.bed.split12306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12307 0 1 2 100 hg38.150200.bed.split12307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12308 0 1 2 100 hg38.150200.bed.split12308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12309 0 1 2 100 hg38.150200.bed.split12309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1231 0 1 2 100 hg38.150200.bed.split1231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12310 0 1 2 100 hg38.150200.bed.split12310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12311 0 1 2 100 hg38.150200.bed.split12311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12312 0 1 2 100 hg38.150200.bed.split12312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12313 0 1 2 100 hg38.150200.bed.split12313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12314 0 1 2 100 hg38.150200.bed.split12314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12315 0 1 2 100 hg38.150200.bed.split12315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12316 0 1 2 100 hg38.150200.bed.split12316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12317 0 1 2 100 hg38.150200.bed.split12317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12318 0 1 2 100 hg38.150200.bed.split12318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12319 0 1 2 100 hg38.150200.bed.split12319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1232 0 1 2 100 hg38.150200.bed.split1232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12320 0 1 2 100 hg38.150200.bed.split12320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12321 0 1 2 100 hg38.150200.bed.split12321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12322 0 1 2 100 hg38.150200.bed.split12322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12323 0 1 2 100 hg38.150200.bed.split12323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12324 0 1 2 100 hg38.150200.bed.split12324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12325 0 1 2 100 hg38.150200.bed.split12325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12326 0 1 2 100 hg38.150200.bed.split12326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12327 0 1 2 100 hg38.150200.bed.split12327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12328 0 1 2 100 hg38.150200.bed.split12328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12329 0 1 2 100 hg38.150200.bed.split12329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1233 0 1 2 100 hg38.150200.bed.split1233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12330 0 1 2 100 hg38.150200.bed.split12330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12331 0 1 2 100 hg38.150200.bed.split12331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12332 0 1 2 100 hg38.150200.bed.split12332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12333 0 1 2 100 hg38.150200.bed.split12333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12334 0 1 2 100 hg38.150200.bed.split12334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12335 0 1 2 100 hg38.150200.bed.split12335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12336 0 1 2 100 hg38.150200.bed.split12336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12337 0 1 2 100 hg38.150200.bed.split12337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12338 0 1 2 100 hg38.150200.bed.split12338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12339 0 1 2 100 hg38.150200.bed.split12339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1234 0 1 2 100 hg38.150200.bed.split1234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12340 0 1 2 100 hg38.150200.bed.split12340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12341 0 1 2 100 hg38.150200.bed.split12341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12342 0 1 2 100 hg38.150200.bed.split12342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12343 0 1 2 100 hg38.150200.bed.split12343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12344 0 1 2 100 hg38.150200.bed.split12344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12345 0 1 2 100 hg38.150200.bed.split12345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12346 0 1 2 100 hg38.150200.bed.split12346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12347 0 1 2 100 hg38.150200.bed.split12347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12348 0 1 2 100 hg38.150200.bed.split12348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12349 0 1 2 100 hg38.150200.bed.split12349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1235 0 1 2 100 hg38.150200.bed.split1235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12350 0 1 2 100 hg38.150200.bed.split12350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12351 0 1 2 100 hg38.150200.bed.split12351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12352 0 1 2 100 hg38.150200.bed.split12352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12353 0 1 2 100 hg38.150200.bed.split12353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12354 0 1 2 100 hg38.150200.bed.split12354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12355 0 1 2 100 hg38.150200.bed.split12355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12356 0 1 2 100 hg38.150200.bed.split12356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12357 0 1 2 100 hg38.150200.bed.split12357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12358 0 1 2 100 hg38.150200.bed.split12358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12359 0 1 2 100 hg38.150200.bed.split12359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1236 0 1 2 100 hg38.150200.bed.split1236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12360 0 1 2 100 hg38.150200.bed.split12360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12361 0 1 2 100 hg38.150200.bed.split12361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12362 0 1 2 100 hg38.150200.bed.split12362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12363 0 1 2 100 hg38.150200.bed.split12363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12364 0 1 2 100 hg38.150200.bed.split12364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12365 0 1 2 100 hg38.150200.bed.split12365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12366 0 1 2 100 hg38.150200.bed.split12366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12367 0 1 2 100 hg38.150200.bed.split12367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12368 0 1 2 100 hg38.150200.bed.split12368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12369 0 1 2 100 hg38.150200.bed.split12369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1237 0 1 2 100 hg38.150200.bed.split1237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12370 0 1 2 100 hg38.150200.bed.split12370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12371 0 1 2 100 hg38.150200.bed.split12371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12372 0 1 2 100 hg38.150200.bed.split12372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12373 0 1 2 100 hg38.150200.bed.split12373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12374 0 1 2 100 hg38.150200.bed.split12374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12375 0 1 2 100 hg38.150200.bed.split12375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12376 0 1 2 100 hg38.150200.bed.split12376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12377 0 1 2 100 hg38.150200.bed.split12377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12378 0 1 2 100 hg38.150200.bed.split12378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12379 0 1 2 100 hg38.150200.bed.split12379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1238 0 1 2 100 hg38.150200.bed.split1238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12380 0 1 2 100 hg38.150200.bed.split12380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12381 0 1 2 100 hg38.150200.bed.split12381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12382 0 1 2 100 hg38.150200.bed.split12382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12383 0 1 2 100 hg38.150200.bed.split12383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12384 0 1 2 100 hg38.150200.bed.split12384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12385 0 1 2 100 hg38.150200.bed.split12385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12386 0 1 2 100 hg38.150200.bed.split12386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12387 0 1 2 100 hg38.150200.bed.split12387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12388 0 1 2 100 hg38.150200.bed.split12388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12389 0 1 2 100 hg38.150200.bed.split12389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1239 0 1 2 100 hg38.150200.bed.split1239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12390 0 1 2 100 hg38.150200.bed.split12390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12391 0 1 2 100 hg38.150200.bed.split12391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12392 0 1 2 100 hg38.150200.bed.split12392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12393 0 1 2 100 hg38.150200.bed.split12393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12394 0 1 2 100 hg38.150200.bed.split12394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12395 0 1 2 100 hg38.150200.bed.split12395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12396 0 1 2 100 hg38.150200.bed.split12396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12397 0 1 2 100 hg38.150200.bed.split12397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12398 0 1 2 100 hg38.150200.bed.split12398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12399 0 1 2 100 hg38.150200.bed.split12399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split124 0 1 2 100 hg38.150200.bed.split124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1240 0 1 2 100 hg38.150200.bed.split1240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12400 0 1 2 100 hg38.150200.bed.split12400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12401 0 1 2 100 hg38.150200.bed.split12401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12402 0 1 2 100 hg38.150200.bed.split12402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12403 0 1 2 100 hg38.150200.bed.split12403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12404 0 1 2 100 hg38.150200.bed.split12404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12405 0 1 2 100 hg38.150200.bed.split12405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12406 0 1 2 100 hg38.150200.bed.split12406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12407 0 1 2 100 hg38.150200.bed.split12407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12408 0 1 2 100 hg38.150200.bed.split12408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12409 0 1 2 100 hg38.150200.bed.split12409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1241 0 1 2 100 hg38.150200.bed.split1241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12410 0 1 2 100 hg38.150200.bed.split12410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12411 0 1 2 100 hg38.150200.bed.split12411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12412 0 1 2 100 hg38.150200.bed.split12412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12413 0 1 2 100 hg38.150200.bed.split12413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12414 0 1 2 100 hg38.150200.bed.split12414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12415 0 1 2 100 hg38.150200.bed.split12415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12416 0 1 2 100 hg38.150200.bed.split12416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12417 0 1 2 100 hg38.150200.bed.split12417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12418 0 1 2 100 hg38.150200.bed.split12418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12419 0 1 2 100 hg38.150200.bed.split12419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1242 0 1 2 100 hg38.150200.bed.split1242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12420 0 1 2 100 hg38.150200.bed.split12420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12421 0 1 2 100 hg38.150200.bed.split12421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12422 0 1 2 100 hg38.150200.bed.split12422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12423 0 1 2 100 hg38.150200.bed.split12423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12424 0 1 2 100 hg38.150200.bed.split12424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12425 0 1 2 100 hg38.150200.bed.split12425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12426 0 1 2 100 hg38.150200.bed.split12426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12427 0 1 2 100 hg38.150200.bed.split12427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12428 0 1 2 100 hg38.150200.bed.split12428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12429 0 1 2 100 hg38.150200.bed.split12429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1243 0 1 2 100 hg38.150200.bed.split1243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12430 0 1 2 100 hg38.150200.bed.split12430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12431 0 1 2 100 hg38.150200.bed.split12431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12432 0 1 2 100 hg38.150200.bed.split12432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12433 0 1 2 100 hg38.150200.bed.split12433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12434 0 1 2 100 hg38.150200.bed.split12434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12435 0 1 2 100 hg38.150200.bed.split12435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12436 0 1 2 100 hg38.150200.bed.split12436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12437 0 1 2 100 hg38.150200.bed.split12437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12438 0 1 2 100 hg38.150200.bed.split12438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12439 0 1 2 100 hg38.150200.bed.split12439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1244 0 1 2 100 hg38.150200.bed.split1244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12440 0 1 2 100 hg38.150200.bed.split12440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12441 0 1 2 100 hg38.150200.bed.split12441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12442 0 1 2 100 hg38.150200.bed.split12442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12443 0 1 2 100 hg38.150200.bed.split12443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12444 0 1 2 100 hg38.150200.bed.split12444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12445 0 1 2 100 hg38.150200.bed.split12445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12446 0 1 2 100 hg38.150200.bed.split12446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12447 0 1 2 100 hg38.150200.bed.split12447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12448 0 1 2 100 hg38.150200.bed.split12448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12449 0 1 2 100 hg38.150200.bed.split12449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1245 0 1 2 100 hg38.150200.bed.split1245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12450 0 1 2 100 hg38.150200.bed.split12450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12451 0 1 2 100 hg38.150200.bed.split12451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12452 0 1 2 100 hg38.150200.bed.split12452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12453 0 1 2 100 hg38.150200.bed.split12453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12454 0 1 2 100 hg38.150200.bed.split12454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12455 0 1 2 100 hg38.150200.bed.split12455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12456 0 1 2 100 hg38.150200.bed.split12456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12457 0 1 2 100 hg38.150200.bed.split12457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12458 0 1 2 100 hg38.150200.bed.split12458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12459 0 1 2 100 hg38.150200.bed.split12459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1246 0 1 2 100 hg38.150200.bed.split1246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12460 0 1 2 100 hg38.150200.bed.split12460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12461 0 1 2 100 hg38.150200.bed.split12461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12462 0 1 2 100 hg38.150200.bed.split12462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12463 0 1 2 100 hg38.150200.bed.split12463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12464 0 1 2 100 hg38.150200.bed.split12464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12465 0 1 2 100 hg38.150200.bed.split12465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12466 0 1 2 100 hg38.150200.bed.split12466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12467 0 1 2 100 hg38.150200.bed.split12467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12468 0 1 2 100 hg38.150200.bed.split12468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12469 0 1 2 100 hg38.150200.bed.split12469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1247 0 1 2 100 hg38.150200.bed.split1247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12470 0 1 2 100 hg38.150200.bed.split12470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12471 0 1 2 100 hg38.150200.bed.split12471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12472 0 1 2 100 hg38.150200.bed.split12472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12473 0 1 2 100 hg38.150200.bed.split12473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12474 0 1 2 100 hg38.150200.bed.split12474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12475 0 1 2 100 hg38.150200.bed.split12475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12476 0 1 2 100 hg38.150200.bed.split12476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12477 0 1 2 100 hg38.150200.bed.split12477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12478 0 1 2 100 hg38.150200.bed.split12478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12479 0 1 2 100 hg38.150200.bed.split12479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1248 0 1 2 100 hg38.150200.bed.split1248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12480 0 1 2 100 hg38.150200.bed.split12480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12481 0 1 2 100 hg38.150200.bed.split12481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12482 0 1 2 100 hg38.150200.bed.split12482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12483 0 1 2 100 hg38.150200.bed.split12483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12484 0 1 2 100 hg38.150200.bed.split12484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12485 0 1 2 100 hg38.150200.bed.split12485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12486 0 1 2 100 hg38.150200.bed.split12486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12487 0 1 2 100 hg38.150200.bed.split12487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12488 0 1 2 100 hg38.150200.bed.split12488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12489 0 1 2 100 hg38.150200.bed.split12489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1249 0 1 2 100 hg38.150200.bed.split1249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12490 0 1 2 100 hg38.150200.bed.split12490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12491 0 1 2 100 hg38.150200.bed.split12491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12492 0 1 2 100 hg38.150200.bed.split12492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12493 0 1 2 100 hg38.150200.bed.split12493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12494 0 1 2 100 hg38.150200.bed.split12494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12495 0 1 2 100 hg38.150200.bed.split12495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12496 0 1 2 100 hg38.150200.bed.split12496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12497 0 1 2 100 hg38.150200.bed.split12497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12498 0 1 2 100 hg38.150200.bed.split12498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12499 0 1 2 100 hg38.150200.bed.split12499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split125 0 1 2 100 hg38.150200.bed.split125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1250 0 1 2 100 hg38.150200.bed.split1250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12500 0 1 2 100 hg38.150200.bed.split12500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12501 0 1 2 100 hg38.150200.bed.split12501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12502 0 1 2 100 hg38.150200.bed.split12502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12503 0 1 2 100 hg38.150200.bed.split12503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12504 0 1 2 100 hg38.150200.bed.split12504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12505 0 1 2 100 hg38.150200.bed.split12505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12506 0 1 2 100 hg38.150200.bed.split12506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12507 0 1 2 100 hg38.150200.bed.split12507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12508 0 1 2 100 hg38.150200.bed.split12508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12509 0 1 2 100 hg38.150200.bed.split12509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1251 0 1 2 100 hg38.150200.bed.split1251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12510 0 1 2 100 hg38.150200.bed.split12510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12511 0 1 2 100 hg38.150200.bed.split12511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12512 0 1 2 100 hg38.150200.bed.split12512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12513 0 1 2 100 hg38.150200.bed.split12513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12514 0 1 2 100 hg38.150200.bed.split12514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12515 0 1 2 100 hg38.150200.bed.split12515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12516 0 1 2 100 hg38.150200.bed.split12516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12517 0 1 2 100 hg38.150200.bed.split12517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12518 0 1 2 100 hg38.150200.bed.split12518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12519 0 1 2 100 hg38.150200.bed.split12519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1252 0 1 2 100 hg38.150200.bed.split1252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12520 0 1 2 100 hg38.150200.bed.split12520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12521 0 1 2 100 hg38.150200.bed.split12521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12522 0 1 2 100 hg38.150200.bed.split12522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12523 0 1 2 100 hg38.150200.bed.split12523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12524 0 1 2 100 hg38.150200.bed.split12524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12525 0 1 2 100 hg38.150200.bed.split12525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12526 0 1 2 100 hg38.150200.bed.split12526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12527 0 1 2 100 hg38.150200.bed.split12527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12528 0 1 2 100 hg38.150200.bed.split12528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12529 0 1 2 100 hg38.150200.bed.split12529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1253 0 1 2 100 hg38.150200.bed.split1253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12530 0 1 2 100 hg38.150200.bed.split12530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12531 0 1 2 100 hg38.150200.bed.split12531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12532 0 1 2 100 hg38.150200.bed.split12532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12533 0 1 2 100 hg38.150200.bed.split12533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12534 0 1 2 100 hg38.150200.bed.split12534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12535 0 1 2 100 hg38.150200.bed.split12535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12536 0 1 2 100 hg38.150200.bed.split12536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12537 0 1 2 100 hg38.150200.bed.split12537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12538 0 1 2 100 hg38.150200.bed.split12538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12539 0 1 2 100 hg38.150200.bed.split12539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1254 0 1 2 100 hg38.150200.bed.split1254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12540 0 1 2 100 hg38.150200.bed.split12540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12541 0 1 2 100 hg38.150200.bed.split12541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12542 0 1 2 100 hg38.150200.bed.split12542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12543 0 1 2 100 hg38.150200.bed.split12543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12544 0 1 2 100 hg38.150200.bed.split12544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12545 0 1 2 100 hg38.150200.bed.split12545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12546 0 1 2 100 hg38.150200.bed.split12546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12547 0 1 2 100 hg38.150200.bed.split12547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12548 0 1 2 100 hg38.150200.bed.split12548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12549 0 1 2 100 hg38.150200.bed.split12549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1255 0 1 2 100 hg38.150200.bed.split1255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12550 0 1 2 100 hg38.150200.bed.split12550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12551 0 1 2 100 hg38.150200.bed.split12551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12552 0 1 2 100 hg38.150200.bed.split12552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12553 0 1 2 100 hg38.150200.bed.split12553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12554 0 1 2 100 hg38.150200.bed.split12554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12555 0 1 2 100 hg38.150200.bed.split12555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12556 0 1 2 100 hg38.150200.bed.split12556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12557 0 1 2 100 hg38.150200.bed.split12557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12558 0 1 2 100 hg38.150200.bed.split12558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12559 0 1 2 100 hg38.150200.bed.split12559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1256 0 1 2 100 hg38.150200.bed.split1256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12560 0 1 2 100 hg38.150200.bed.split12560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12561 0 1 2 100 hg38.150200.bed.split12561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12562 0 1 2 100 hg38.150200.bed.split12562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12563 0 1 2 100 hg38.150200.bed.split12563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12564 0 1 2 100 hg38.150200.bed.split12564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12565 0 1 2 100 hg38.150200.bed.split12565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12566 0 1 2 100 hg38.150200.bed.split12566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12567 0 1 2 100 hg38.150200.bed.split12567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12568 0 1 2 100 hg38.150200.bed.split12568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12569 0 1 2 100 hg38.150200.bed.split12569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1257 0 1 2 100 hg38.150200.bed.split1257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12570 0 1 2 100 hg38.150200.bed.split12570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12571 0 1 2 100 hg38.150200.bed.split12571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12572 0 1 2 100 hg38.150200.bed.split12572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12573 0 1 2 100 hg38.150200.bed.split12573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12574 0 1 2 100 hg38.150200.bed.split12574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12575 0 1 2 100 hg38.150200.bed.split12575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12576 0 1 2 100 hg38.150200.bed.split12576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12577 0 1 2 100 hg38.150200.bed.split12577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12578 0 1 2 100 hg38.150200.bed.split12578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12579 0 1 2 100 hg38.150200.bed.split12579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1258 0 1 2 100 hg38.150200.bed.split1258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12580 0 1 2 100 hg38.150200.bed.split12580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12581 0 1 2 100 hg38.150200.bed.split12581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12582 0 1 2 100 hg38.150200.bed.split12582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12583 0 1 2 100 hg38.150200.bed.split12583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12584 0 1 2 100 hg38.150200.bed.split12584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12585 0 1 2 100 hg38.150200.bed.split12585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12586 0 1 2 100 hg38.150200.bed.split12586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12587 0 1 2 100 hg38.150200.bed.split12587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12588 0 1 2 100 hg38.150200.bed.split12588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12589 0 1 2 100 hg38.150200.bed.split12589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1259 0 1 2 100 hg38.150200.bed.split1259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12590 0 1 2 100 hg38.150200.bed.split12590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12591 0 1 2 100 hg38.150200.bed.split12591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12592 0 1 2 100 hg38.150200.bed.split12592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12593 0 1 2 100 hg38.150200.bed.split12593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12594 0 1 2 100 hg38.150200.bed.split12594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12595 0 1 2 100 hg38.150200.bed.split12595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12596 0 1 2 100 hg38.150200.bed.split12596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12597 0 1 2 100 hg38.150200.bed.split12597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12598 0 1 2 100 hg38.150200.bed.split12598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12599 0 1 2 100 hg38.150200.bed.split12599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split126 0 1 2 100 hg38.150200.bed.split126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1260 0 1 2 100 hg38.150200.bed.split1260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12600 0 1 2 100 hg38.150200.bed.split12600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12601 0 1 2 100 hg38.150200.bed.split12601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12602 0 1 2 100 hg38.150200.bed.split12602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12603 0 1 2 100 hg38.150200.bed.split12603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12604 0 1 2 100 hg38.150200.bed.split12604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12605 0 1 2 100 hg38.150200.bed.split12605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12606 0 1 2 100 hg38.150200.bed.split12606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12607 0 1 2 100 hg38.150200.bed.split12607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12608 0 1 2 100 hg38.150200.bed.split12608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12609 0 1 2 100 hg38.150200.bed.split12609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1261 0 1 2 100 hg38.150200.bed.split1261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12610 0 1 2 100 hg38.150200.bed.split12610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12611 0 1 2 100 hg38.150200.bed.split12611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12612 0 1 2 100 hg38.150200.bed.split12612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12613 0 1 2 100 hg38.150200.bed.split12613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12614 0 1 2 100 hg38.150200.bed.split12614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12615 0 1 2 100 hg38.150200.bed.split12615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12616 0 1 2 100 hg38.150200.bed.split12616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12617 0 1 2 100 hg38.150200.bed.split12617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12618 0 1 2 100 hg38.150200.bed.split12618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12619 0 1 2 100 hg38.150200.bed.split12619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1262 0 1 2 100 hg38.150200.bed.split1262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12620 0 1 2 100 hg38.150200.bed.split12620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12621 0 1 2 100 hg38.150200.bed.split12621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12622 0 1 2 100 hg38.150200.bed.split12622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12623 0 1 2 100 hg38.150200.bed.split12623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12624 0 1 2 100 hg38.150200.bed.split12624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12625 0 1 2 100 hg38.150200.bed.split12625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12626 0 1 2 100 hg38.150200.bed.split12626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12627 0 1 2 100 hg38.150200.bed.split12627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12628 0 1 2 100 hg38.150200.bed.split12628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12629 0 1 2 100 hg38.150200.bed.split12629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1263 0 1 2 100 hg38.150200.bed.split1263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12630 0 1 2 100 hg38.150200.bed.split12630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12631 0 1 2 100 hg38.150200.bed.split12631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12632 0 1 2 100 hg38.150200.bed.split12632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12633 0 1 2 100 hg38.150200.bed.split12633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12634 0 1 2 100 hg38.150200.bed.split12634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12635 0 1 2 100 hg38.150200.bed.split12635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12636 0 1 2 100 hg38.150200.bed.split12636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12637 0 1 2 100 hg38.150200.bed.split12637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12638 0 1 2 100 hg38.150200.bed.split12638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12639 0 1 2 100 hg38.150200.bed.split12639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1264 0 1 2 100 hg38.150200.bed.split1264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12640 0 1 2 100 hg38.150200.bed.split12640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12641 0 1 2 100 hg38.150200.bed.split12641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12642 0 1 2 100 hg38.150200.bed.split12642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12643 0 1 2 100 hg38.150200.bed.split12643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12644 0 1 2 100 hg38.150200.bed.split12644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12645 0 1 2 100 hg38.150200.bed.split12645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12646 0 1 2 100 hg38.150200.bed.split12646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12647 0 1 2 100 hg38.150200.bed.split12647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12648 0 1 2 100 hg38.150200.bed.split12648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12649 0 1 2 100 hg38.150200.bed.split12649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1265 0 1 2 100 hg38.150200.bed.split1265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12650 0 1 2 100 hg38.150200.bed.split12650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12651 0 1 2 100 hg38.150200.bed.split12651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12652 0 1 2 100 hg38.150200.bed.split12652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12653 0 1 2 100 hg38.150200.bed.split12653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12654 0 1 2 100 hg38.150200.bed.split12654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12655 0 1 2 100 hg38.150200.bed.split12655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12656 0 1 2 100 hg38.150200.bed.split12656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12657 0 1 2 100 hg38.150200.bed.split12657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12658 0 1 2 100 hg38.150200.bed.split12658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12659 0 1 2 100 hg38.150200.bed.split12659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1266 0 1 2 100 hg38.150200.bed.split1266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12660 0 1 2 100 hg38.150200.bed.split12660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12661 0 1 2 100 hg38.150200.bed.split12661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12662 0 1 2 100 hg38.150200.bed.split12662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12663 0 1 2 100 hg38.150200.bed.split12663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12664 0 1 2 100 hg38.150200.bed.split12664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12665 0 1 2 100 hg38.150200.bed.split12665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12666 0 1 2 100 hg38.150200.bed.split12666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12667 0 1 2 100 hg38.150200.bed.split12667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12668 0 1 2 100 hg38.150200.bed.split12668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12669 0 1 2 100 hg38.150200.bed.split12669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1267 0 1 2 100 hg38.150200.bed.split1267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12670 0 1 2 100 hg38.150200.bed.split12670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12671 0 1 2 100 hg38.150200.bed.split12671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12672 0 1 2 100 hg38.150200.bed.split12672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12673 0 1 2 100 hg38.150200.bed.split12673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12674 0 1 2 100 hg38.150200.bed.split12674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12675 0 1 2 100 hg38.150200.bed.split12675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12676 0 1 2 100 hg38.150200.bed.split12676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12677 0 1 2 100 hg38.150200.bed.split12677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12678 0 1 2 100 hg38.150200.bed.split12678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12679 0 1 2 100 hg38.150200.bed.split12679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1268 0 1 2 100 hg38.150200.bed.split1268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12680 0 1 2 100 hg38.150200.bed.split12680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12681 0 1 2 100 hg38.150200.bed.split12681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12682 0 1 2 100 hg38.150200.bed.split12682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12683 0 1 2 100 hg38.150200.bed.split12683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12684 0 1 2 100 hg38.150200.bed.split12684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12685 0 1 2 100 hg38.150200.bed.split12685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12686 0 1 2 100 hg38.150200.bed.split12686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12687 0 1 2 100 hg38.150200.bed.split12687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12688 0 1 2 100 hg38.150200.bed.split12688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12689 0 1 2 100 hg38.150200.bed.split12689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1269 0 1 2 100 hg38.150200.bed.split1269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12690 0 1 2 100 hg38.150200.bed.split12690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12691 0 1 2 100 hg38.150200.bed.split12691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12692 0 1 2 100 hg38.150200.bed.split12692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12693 0 1 2 100 hg38.150200.bed.split12693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12694 0 1 2 100 hg38.150200.bed.split12694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12695 0 1 2 100 hg38.150200.bed.split12695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12696 0 1 2 100 hg38.150200.bed.split12696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12697 0 1 2 100 hg38.150200.bed.split12697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12698 0 1 2 100 hg38.150200.bed.split12698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12699 0 1 2 100 hg38.150200.bed.split12699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split127 0 1 2 100 hg38.150200.bed.split127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1270 0 1 2 100 hg38.150200.bed.split1270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12700 0 1 2 100 hg38.150200.bed.split12700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12701 0 1 2 100 hg38.150200.bed.split12701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12702 0 1 2 100 hg38.150200.bed.split12702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12703 0 1 2 100 hg38.150200.bed.split12703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12704 0 1 2 100 hg38.150200.bed.split12704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12705 0 1 2 100 hg38.150200.bed.split12705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12706 0 1 2 100 hg38.150200.bed.split12706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12707 0 1 2 100 hg38.150200.bed.split12707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12708 0 1 2 100 hg38.150200.bed.split12708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12709 0 1 2 100 hg38.150200.bed.split12709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1271 0 1 2 100 hg38.150200.bed.split1271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12710 0 1 2 100 hg38.150200.bed.split12710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12711 0 1 2 100 hg38.150200.bed.split12711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12712 0 1 2 100 hg38.150200.bed.split12712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12713 0 1 2 100 hg38.150200.bed.split12713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12714 0 1 2 100 hg38.150200.bed.split12714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12715 0 1 2 100 hg38.150200.bed.split12715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12716 0 1 2 100 hg38.150200.bed.split12716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12717 0 1 2 100 hg38.150200.bed.split12717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12718 0 1 2 100 hg38.150200.bed.split12718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12719 0 1 2 100 hg38.150200.bed.split12719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1272 0 1 2 100 hg38.150200.bed.split1272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12720 0 1 2 100 hg38.150200.bed.split12720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12721 0 1 2 100 hg38.150200.bed.split12721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12722 0 1 2 100 hg38.150200.bed.split12722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12723 0 1 2 100 hg38.150200.bed.split12723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12724 0 1 2 100 hg38.150200.bed.split12724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12725 0 1 2 100 hg38.150200.bed.split12725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12726 0 1 2 100 hg38.150200.bed.split12726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12727 0 1 2 100 hg38.150200.bed.split12727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12728 0 1 2 100 hg38.150200.bed.split12728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12729 0 1 2 100 hg38.150200.bed.split12729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1273 0 1 2 100 hg38.150200.bed.split1273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12730 0 1 2 100 hg38.150200.bed.split12730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12731 0 1 2 100 hg38.150200.bed.split12731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12732 0 1 2 100 hg38.150200.bed.split12732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12733 0 1 2 100 hg38.150200.bed.split12733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12734 0 1 2 100 hg38.150200.bed.split12734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12735 0 1 2 100 hg38.150200.bed.split12735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12736 0 1 2 100 hg38.150200.bed.split12736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12737 0 1 2 100 hg38.150200.bed.split12737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12738 0 1 2 100 hg38.150200.bed.split12738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12739 0 1 2 100 hg38.150200.bed.split12739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1274 0 1 2 100 hg38.150200.bed.split1274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12740 0 1 2 100 hg38.150200.bed.split12740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12741 0 1 2 100 hg38.150200.bed.split12741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12742 0 1 2 100 hg38.150200.bed.split12742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12743 0 1 2 100 hg38.150200.bed.split12743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12744 0 1 2 100 hg38.150200.bed.split12744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12745 0 1 2 100 hg38.150200.bed.split12745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12746 0 1 2 100 hg38.150200.bed.split12746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12747 0 1 2 100 hg38.150200.bed.split12747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12748 0 1 2 100 hg38.150200.bed.split12748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12749 0 1 2 100 hg38.150200.bed.split12749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1275 0 1 2 100 hg38.150200.bed.split1275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12750 0 1 2 100 hg38.150200.bed.split12750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12751 0 1 2 100 hg38.150200.bed.split12751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12752 0 1 2 100 hg38.150200.bed.split12752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12753 0 1 2 100 hg38.150200.bed.split12753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12754 0 1 2 100 hg38.150200.bed.split12754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12755 0 1 2 100 hg38.150200.bed.split12755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12756 0 1 2 100 hg38.150200.bed.split12756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12757 0 1 2 100 hg38.150200.bed.split12757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12758 0 1 2 100 hg38.150200.bed.split12758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12759 0 1 2 100 hg38.150200.bed.split12759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1276 0 1 2 100 hg38.150200.bed.split1276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12760 0 1 2 100 hg38.150200.bed.split12760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12761 0 1 2 100 hg38.150200.bed.split12761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12762 0 1 2 100 hg38.150200.bed.split12762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12763 0 1 2 100 hg38.150200.bed.split12763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12764 0 1 2 100 hg38.150200.bed.split12764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12765 0 1 2 100 hg38.150200.bed.split12765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12766 0 1 2 100 hg38.150200.bed.split12766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12767 0 1 2 100 hg38.150200.bed.split12767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12768 0 1 2 100 hg38.150200.bed.split12768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12769 0 1 2 100 hg38.150200.bed.split12769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1277 0 1 2 100 hg38.150200.bed.split1277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12770 0 1 2 100 hg38.150200.bed.split12770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12771 0 1 2 100 hg38.150200.bed.split12771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12772 0 1 2 100 hg38.150200.bed.split12772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12773 0 1 2 100 hg38.150200.bed.split12773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12774 0 1 2 100 hg38.150200.bed.split12774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12775 0 1 2 100 hg38.150200.bed.split12775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12776 0 1 2 100 hg38.150200.bed.split12776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12777 0 1 2 100 hg38.150200.bed.split12777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12778 0 1 2 100 hg38.150200.bed.split12778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12779 0 1 2 100 hg38.150200.bed.split12779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1278 0 1 2 100 hg38.150200.bed.split1278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12780 0 1 2 100 hg38.150200.bed.split12780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12781 0 1 2 100 hg38.150200.bed.split12781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12782 0 1 2 100 hg38.150200.bed.split12782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12783 0 1 2 100 hg38.150200.bed.split12783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12784 0 1 2 100 hg38.150200.bed.split12784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12785 0 1 2 100 hg38.150200.bed.split12785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12786 0 1 2 100 hg38.150200.bed.split12786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12787 0 1 2 100 hg38.150200.bed.split12787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12788 0 1 2 100 hg38.150200.bed.split12788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12789 0 1 2 100 hg38.150200.bed.split12789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1279 0 1 2 100 hg38.150200.bed.split1279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12790 0 1 2 100 hg38.150200.bed.split12790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12791 0 1 2 100 hg38.150200.bed.split12791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12792 0 1 2 100 hg38.150200.bed.split12792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12793 0 1 2 100 hg38.150200.bed.split12793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12794 0 1 2 100 hg38.150200.bed.split12794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12795 0 1 2 100 hg38.150200.bed.split12795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12796 0 1 2 100 hg38.150200.bed.split12796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12797 0 1 2 100 hg38.150200.bed.split12797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12798 0 1 2 100 hg38.150200.bed.split12798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12799 0 1 2 100 hg38.150200.bed.split12799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split128 0 1 2 100 hg38.150200.bed.split128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1280 0 1 2 100 hg38.150200.bed.split1280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12800 0 1 2 100 hg38.150200.bed.split12800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12801 0 1 2 100 hg38.150200.bed.split12801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12802 0 1 2 100 hg38.150200.bed.split12802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12803 0 1 2 100 hg38.150200.bed.split12803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12804 0 1 2 100 hg38.150200.bed.split12804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12805 0 1 2 100 hg38.150200.bed.split12805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12806 0 1 2 100 hg38.150200.bed.split12806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12807 0 1 2 100 hg38.150200.bed.split12807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12808 0 1 2 100 hg38.150200.bed.split12808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12809 0 1 2 100 hg38.150200.bed.split12809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1281 0 1 2 100 hg38.150200.bed.split1281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12810 0 1 2 100 hg38.150200.bed.split12810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12811 0 1 2 100 hg38.150200.bed.split12811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12812 0 1 2 100 hg38.150200.bed.split12812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12813 0 1 2 100 hg38.150200.bed.split12813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12814 0 1 2 100 hg38.150200.bed.split12814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12815 0 1 2 100 hg38.150200.bed.split12815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12816 0 1 2 100 hg38.150200.bed.split12816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12817 0 1 2 100 hg38.150200.bed.split12817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12818 0 1 2 100 hg38.150200.bed.split12818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12819 0 1 2 100 hg38.150200.bed.split12819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1282 0 1 2 100 hg38.150200.bed.split1282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12820 0 1 2 100 hg38.150200.bed.split12820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12821 0 1 2 100 hg38.150200.bed.split12821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12822 0 1 2 100 hg38.150200.bed.split12822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12823 0 1 2 100 hg38.150200.bed.split12823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12824 0 1 2 100 hg38.150200.bed.split12824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12825 0 1 2 100 hg38.150200.bed.split12825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12826 0 1 2 100 hg38.150200.bed.split12826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12827 0 1 2 100 hg38.150200.bed.split12827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12828 0 1 2 100 hg38.150200.bed.split12828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12829 0 1 2 100 hg38.150200.bed.split12829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1283 0 1 2 100 hg38.150200.bed.split1283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12830 0 1 2 100 hg38.150200.bed.split12830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12831 0 1 2 100 hg38.150200.bed.split12831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12832 0 1 2 100 hg38.150200.bed.split12832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12833 0 1 2 100 hg38.150200.bed.split12833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12834 0 1 2 100 hg38.150200.bed.split12834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12835 0 1 2 100 hg38.150200.bed.split12835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12836 0 1 2 100 hg38.150200.bed.split12836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12837 0 1 2 100 hg38.150200.bed.split12837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12838 0 1 2 100 hg38.150200.bed.split12838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12839 0 1 2 100 hg38.150200.bed.split12839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1284 0 1 2 100 hg38.150200.bed.split1284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12840 0 1 2 100 hg38.150200.bed.split12840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12841 0 1 2 100 hg38.150200.bed.split12841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12842 0 1 2 100 hg38.150200.bed.split12842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12843 0 1 2 100 hg38.150200.bed.split12843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12844 0 1 2 100 hg38.150200.bed.split12844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12845 0 1 2 100 hg38.150200.bed.split12845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12846 0 1 2 100 hg38.150200.bed.split12846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12847 0 1 2 100 hg38.150200.bed.split12847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12848 0 1 2 100 hg38.150200.bed.split12848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12849 0 1 2 100 hg38.150200.bed.split12849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1285 0 1 2 100 hg38.150200.bed.split1285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12850 0 1 2 100 hg38.150200.bed.split12850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12851 0 1 2 100 hg38.150200.bed.split12851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12852 0 1 2 100 hg38.150200.bed.split12852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12853 0 1 2 100 hg38.150200.bed.split12853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12854 0 1 2 100 hg38.150200.bed.split12854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12855 0 1 2 100 hg38.150200.bed.split12855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12856 0 1 2 100 hg38.150200.bed.split12856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12857 0 1 2 100 hg38.150200.bed.split12857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12858 0 1 2 100 hg38.150200.bed.split12858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12859 0 1 2 100 hg38.150200.bed.split12859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1286 0 1 2 100 hg38.150200.bed.split1286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12860 0 1 2 100 hg38.150200.bed.split12860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12861 0 1 2 100 hg38.150200.bed.split12861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12862 0 1 2 100 hg38.150200.bed.split12862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12863 0 1 2 100 hg38.150200.bed.split12863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12864 0 1 2 100 hg38.150200.bed.split12864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12865 0 1 2 100 hg38.150200.bed.split12865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12866 0 1 2 100 hg38.150200.bed.split12866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12867 0 1 2 100 hg38.150200.bed.split12867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12868 0 1 2 100 hg38.150200.bed.split12868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12869 0 1 2 100 hg38.150200.bed.split12869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1287 0 1 2 100 hg38.150200.bed.split1287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12870 0 1 2 100 hg38.150200.bed.split12870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12871 0 1 2 100 hg38.150200.bed.split12871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12872 0 1 2 100 hg38.150200.bed.split12872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12873 0 1 2 100 hg38.150200.bed.split12873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12874 0 1 2 100 hg38.150200.bed.split12874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12875 0 1 2 100 hg38.150200.bed.split12875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12876 0 1 2 100 hg38.150200.bed.split12876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12877 0 1 2 100 hg38.150200.bed.split12877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12878 0 1 2 100 hg38.150200.bed.split12878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12879 0 1 2 100 hg38.150200.bed.split12879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1288 0 1 2 100 hg38.150200.bed.split1288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12880 0 1 2 100 hg38.150200.bed.split12880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12881 0 1 2 100 hg38.150200.bed.split12881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12882 0 1 2 100 hg38.150200.bed.split12882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12883 0 1 2 100 hg38.150200.bed.split12883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12884 0 1 2 100 hg38.150200.bed.split12884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12885 0 1 2 100 hg38.150200.bed.split12885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12886 0 1 2 100 hg38.150200.bed.split12886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12887 0 1 2 100 hg38.150200.bed.split12887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12888 0 1 2 100 hg38.150200.bed.split12888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12889 0 1 2 100 hg38.150200.bed.split12889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1289 0 1 2 100 hg38.150200.bed.split1289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12890 0 1 2 100 hg38.150200.bed.split12890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12891 0 1 2 100 hg38.150200.bed.split12891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12892 0 1 2 100 hg38.150200.bed.split12892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12893 0 1 2 100 hg38.150200.bed.split12893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12894 0 1 2 100 hg38.150200.bed.split12894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12895 0 1 2 100 hg38.150200.bed.split12895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12896 0 1 2 100 hg38.150200.bed.split12896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12897 0 1 2 100 hg38.150200.bed.split12897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12898 0 1 2 100 hg38.150200.bed.split12898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12899 0 1 2 100 hg38.150200.bed.split12899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split129 0 1 2 100 hg38.150200.bed.split129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1290 0 1 2 100 hg38.150200.bed.split1290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12900 0 1 2 100 hg38.150200.bed.split12900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12901 0 1 2 100 hg38.150200.bed.split12901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12902 0 1 2 100 hg38.150200.bed.split12902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12903 0 1 2 100 hg38.150200.bed.split12903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12904 0 1 2 100 hg38.150200.bed.split12904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12905 0 1 2 100 hg38.150200.bed.split12905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12906 0 1 2 100 hg38.150200.bed.split12906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12907 0 1 2 100 hg38.150200.bed.split12907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12908 0 1 2 100 hg38.150200.bed.split12908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12909 0 1 2 100 hg38.150200.bed.split12909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1291 0 1 2 100 hg38.150200.bed.split1291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12910 0 1 2 100 hg38.150200.bed.split12910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12911 0 1 2 100 hg38.150200.bed.split12911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12912 0 1 2 100 hg38.150200.bed.split12912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12913 0 1 2 100 hg38.150200.bed.split12913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12914 0 1 2 100 hg38.150200.bed.split12914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12915 0 1 2 100 hg38.150200.bed.split12915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12916 0 1 2 100 hg38.150200.bed.split12916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12917 0 1 2 100 hg38.150200.bed.split12917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12918 0 1 2 100 hg38.150200.bed.split12918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12919 0 1 2 100 hg38.150200.bed.split12919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1292 0 1 2 100 hg38.150200.bed.split1292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12920 0 1 2 100 hg38.150200.bed.split12920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12921 0 1 2 100 hg38.150200.bed.split12921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12922 0 1 2 100 hg38.150200.bed.split12922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12923 0 1 2 100 hg38.150200.bed.split12923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12924 0 1 2 100 hg38.150200.bed.split12924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12925 0 1 2 100 hg38.150200.bed.split12925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12926 0 1 2 100 hg38.150200.bed.split12926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12927 0 1 2 100 hg38.150200.bed.split12927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12928 0 1 2 100 hg38.150200.bed.split12928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12929 0 1 2 100 hg38.150200.bed.split12929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1293 0 1 2 100 hg38.150200.bed.split1293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12930 0 1 2 100 hg38.150200.bed.split12930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12931 0 1 2 100 hg38.150200.bed.split12931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12932 0 1 2 100 hg38.150200.bed.split12932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12933 0 1 2 100 hg38.150200.bed.split12933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12934 0 1 2 100 hg38.150200.bed.split12934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12935 0 1 2 100 hg38.150200.bed.split12935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12936 0 1 2 100 hg38.150200.bed.split12936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12937 0 1 2 100 hg38.150200.bed.split12937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12938 0 1 2 100 hg38.150200.bed.split12938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12939 0 1 2 100 hg38.150200.bed.split12939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1294 0 1 2 100 hg38.150200.bed.split1294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12940 0 1 2 100 hg38.150200.bed.split12940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12941 0 1 2 100 hg38.150200.bed.split12941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12942 0 1 2 100 hg38.150200.bed.split12942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12943 0 1 2 100 hg38.150200.bed.split12943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12944 0 1 2 100 hg38.150200.bed.split12944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12945 0 1 2 100 hg38.150200.bed.split12945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12946 0 1 2 100 hg38.150200.bed.split12946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12947 0 1 2 100 hg38.150200.bed.split12947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12948 0 1 2 100 hg38.150200.bed.split12948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12949 0 1 2 100 hg38.150200.bed.split12949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1295 0 1 2 100 hg38.150200.bed.split1295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12950 0 1 2 100 hg38.150200.bed.split12950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12951 0 1 2 100 hg38.150200.bed.split12951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12952 0 1 2 100 hg38.150200.bed.split12952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12953 0 1 2 100 hg38.150200.bed.split12953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12954 0 1 2 100 hg38.150200.bed.split12954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12955 0 1 2 100 hg38.150200.bed.split12955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12956 0 1 2 100 hg38.150200.bed.split12956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12957 0 1 2 100 hg38.150200.bed.split12957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12958 0 1 2 100 hg38.150200.bed.split12958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12959 0 1 2 100 hg38.150200.bed.split12959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1296 0 1 2 100 hg38.150200.bed.split1296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12960 0 1 2 100 hg38.150200.bed.split12960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12961 0 1 2 100 hg38.150200.bed.split12961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12962 0 1 2 100 hg38.150200.bed.split12962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12963 0 1 2 100 hg38.150200.bed.split12963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12964 0 1 2 100 hg38.150200.bed.split12964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12965 0 1 2 100 hg38.150200.bed.split12965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12966 0 1 2 100 hg38.150200.bed.split12966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12967 0 1 2 100 hg38.150200.bed.split12967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12968 0 1 2 100 hg38.150200.bed.split12968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12969 0 1 2 100 hg38.150200.bed.split12969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1297 0 1 2 100 hg38.150200.bed.split1297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12970 0 1 2 100 hg38.150200.bed.split12970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12971 0 1 2 100 hg38.150200.bed.split12971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12972 0 1 2 100 hg38.150200.bed.split12972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12973 0 1 2 100 hg38.150200.bed.split12973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12974 0 1 2 100 hg38.150200.bed.split12974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12975 0 1 2 100 hg38.150200.bed.split12975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12976 0 1 2 100 hg38.150200.bed.split12976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12977 0 1 2 100 hg38.150200.bed.split12977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12978 0 1 2 100 hg38.150200.bed.split12978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12979 0 1 2 100 hg38.150200.bed.split12979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1298 0 1 2 100 hg38.150200.bed.split1298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12980 0 1 2 100 hg38.150200.bed.split12980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12981 0 1 2 100 hg38.150200.bed.split12981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12982 0 1 2 100 hg38.150200.bed.split12982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12983 0 1 2 100 hg38.150200.bed.split12983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12984 0 1 2 100 hg38.150200.bed.split12984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12985 0 1 2 100 hg38.150200.bed.split12985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12986 0 1 2 100 hg38.150200.bed.split12986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12987 0 1 2 100 hg38.150200.bed.split12987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12988 0 1 2 100 hg38.150200.bed.split12988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12989 0 1 2 100 hg38.150200.bed.split12989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1299 0 1 2 100 hg38.150200.bed.split1299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12990 0 1 2 100 hg38.150200.bed.split12990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12991 0 1 2 100 hg38.150200.bed.split12991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12992 0 1 2 100 hg38.150200.bed.split12992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12993 0 1 2 100 hg38.150200.bed.split12993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12994 0 1 2 100 hg38.150200.bed.split12994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12995 0 1 2 100 hg38.150200.bed.split12995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12996 0 1 2 100 hg38.150200.bed.split12996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12997 0 1 2 100 hg38.150200.bed.split12997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12998 0 1 2 100 hg38.150200.bed.split12998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split12999 0 1 2 100 hg38.150200.bed.split12999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13 0 1 2 100 hg38.150200.bed.split13.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split130 0 1 2 100 hg38.150200.bed.split130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1300 0 1 2 100 hg38.150200.bed.split1300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13000 0 1 2 100 hg38.150200.bed.split13000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13001 0 1 2 100 hg38.150200.bed.split13001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13002 0 1 2 100 hg38.150200.bed.split13002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13003 0 1 2 100 hg38.150200.bed.split13003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13004 0 1 2 100 hg38.150200.bed.split13004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13005 0 1 2 100 hg38.150200.bed.split13005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13006 0 1 2 100 hg38.150200.bed.split13006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13007 0 1 2 100 hg38.150200.bed.split13007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13008 0 1 2 100 hg38.150200.bed.split13008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13009 0 1 2 100 hg38.150200.bed.split13009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1301 0 1 2 100 hg38.150200.bed.split1301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13010 0 1 2 100 hg38.150200.bed.split13010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13011 0 1 2 100 hg38.150200.bed.split13011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13012 0 1 2 100 hg38.150200.bed.split13012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13013 0 1 2 100 hg38.150200.bed.split13013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13014 0 1 2 100 hg38.150200.bed.split13014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13015 0 1 2 100 hg38.150200.bed.split13015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13016 0 1 2 100 hg38.150200.bed.split13016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13017 0 1 2 100 hg38.150200.bed.split13017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13018 0 1 2 100 hg38.150200.bed.split13018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13019 0 1 2 100 hg38.150200.bed.split13019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1302 0 1 2 100 hg38.150200.bed.split1302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13020 0 1 2 100 hg38.150200.bed.split13020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13021 0 1 2 100 hg38.150200.bed.split13021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13022 0 1 2 100 hg38.150200.bed.split13022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13023 0 1 2 100 hg38.150200.bed.split13023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13024 0 1 2 100 hg38.150200.bed.split13024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13025 0 1 2 100 hg38.150200.bed.split13025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13026 0 1 2 100 hg38.150200.bed.split13026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13027 0 1 2 100 hg38.150200.bed.split13027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13028 0 1 2 100 hg38.150200.bed.split13028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13029 0 1 2 100 hg38.150200.bed.split13029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1303 0 1 2 100 hg38.150200.bed.split1303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13030 0 1 2 100 hg38.150200.bed.split13030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13031 0 1 2 100 hg38.150200.bed.split13031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13032 0 1 2 100 hg38.150200.bed.split13032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13033 0 1 2 100 hg38.150200.bed.split13033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13034 0 1 2 100 hg38.150200.bed.split13034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13035 0 1 2 100 hg38.150200.bed.split13035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13036 0 1 2 100 hg38.150200.bed.split13036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13037 0 1 2 100 hg38.150200.bed.split13037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13038 0 1 2 100 hg38.150200.bed.split13038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13039 0 1 2 100 hg38.150200.bed.split13039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1304 0 1 2 100 hg38.150200.bed.split1304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13040 0 1 2 100 hg38.150200.bed.split13040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13041 0 1 2 100 hg38.150200.bed.split13041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13042 0 1 2 100 hg38.150200.bed.split13042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13043 0 1 2 100 hg38.150200.bed.split13043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13044 0 1 2 100 hg38.150200.bed.split13044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13045 0 1 2 100 hg38.150200.bed.split13045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13046 0 1 2 100 hg38.150200.bed.split13046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13047 0 1 2 100 hg38.150200.bed.split13047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13048 0 1 2 100 hg38.150200.bed.split13048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13049 0 1 2 100 hg38.150200.bed.split13049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1305 0 1 2 100 hg38.150200.bed.split1305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13050 0 1 2 100 hg38.150200.bed.split13050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13051 0 1 2 100 hg38.150200.bed.split13051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13052 0 1 2 100 hg38.150200.bed.split13052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13053 0 1 2 100 hg38.150200.bed.split13053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13054 0 1 2 100 hg38.150200.bed.split13054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13055 0 1 2 100 hg38.150200.bed.split13055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13056 0 1 2 100 hg38.150200.bed.split13056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13057 0 1 2 100 hg38.150200.bed.split13057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13058 0 1 2 100 hg38.150200.bed.split13058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13059 0 1 2 100 hg38.150200.bed.split13059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1306 0 1 2 100 hg38.150200.bed.split1306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13060 0 1 2 100 hg38.150200.bed.split13060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13061 0 1 2 100 hg38.150200.bed.split13061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13062 0 1 2 100 hg38.150200.bed.split13062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13063 0 1 2 100 hg38.150200.bed.split13063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13064 0 1 2 100 hg38.150200.bed.split13064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13065 0 1 2 100 hg38.150200.bed.split13065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13066 0 1 2 100 hg38.150200.bed.split13066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13067 0 1 2 100 hg38.150200.bed.split13067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13068 0 1 2 100 hg38.150200.bed.split13068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13069 0 1 2 100 hg38.150200.bed.split13069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1307 0 1 2 100 hg38.150200.bed.split1307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13070 0 1 2 100 hg38.150200.bed.split13070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13071 0 1 2 100 hg38.150200.bed.split13071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13072 0 1 2 100 hg38.150200.bed.split13072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13073 0 1 2 100 hg38.150200.bed.split13073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13074 0 1 2 100 hg38.150200.bed.split13074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13075 0 1 2 100 hg38.150200.bed.split13075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13076 0 1 2 100 hg38.150200.bed.split13076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13077 0 1 2 100 hg38.150200.bed.split13077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13078 0 1 2 100 hg38.150200.bed.split13078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13079 0 1 2 100 hg38.150200.bed.split13079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1308 0 1 2 100 hg38.150200.bed.split1308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13080 0 1 2 100 hg38.150200.bed.split13080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13081 0 1 2 100 hg38.150200.bed.split13081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13082 0 1 2 100 hg38.150200.bed.split13082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13083 0 1 2 100 hg38.150200.bed.split13083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13084 0 1 2 100 hg38.150200.bed.split13084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13085 0 1 2 100 hg38.150200.bed.split13085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13086 0 1 2 100 hg38.150200.bed.split13086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13087 0 1 2 100 hg38.150200.bed.split13087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13088 0 1 2 100 hg38.150200.bed.split13088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13089 0 1 2 100 hg38.150200.bed.split13089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1309 0 1 2 100 hg38.150200.bed.split1309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13090 0 1 2 100 hg38.150200.bed.split13090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13091 0 1 2 100 hg38.150200.bed.split13091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13092 0 1 2 100 hg38.150200.bed.split13092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13093 0 1 2 100 hg38.150200.bed.split13093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13094 0 1 2 100 hg38.150200.bed.split13094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13095 0 1 2 100 hg38.150200.bed.split13095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13096 0 1 2 100 hg38.150200.bed.split13096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13097 0 1 2 100 hg38.150200.bed.split13097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13098 0 1 2 100 hg38.150200.bed.split13098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13099 0 1 2 100 hg38.150200.bed.split13099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split131 0 1 2 100 hg38.150200.bed.split131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1310 0 1 2 100 hg38.150200.bed.split1310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13100 0 1 2 100 hg38.150200.bed.split13100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13101 0 1 2 100 hg38.150200.bed.split13101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13102 0 1 2 100 hg38.150200.bed.split13102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13103 0 1 2 100 hg38.150200.bed.split13103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13104 0 1 2 100 hg38.150200.bed.split13104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13105 0 1 2 100 hg38.150200.bed.split13105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13106 0 1 2 100 hg38.150200.bed.split13106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13107 0 1 2 100 hg38.150200.bed.split13107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13108 0 1 2 100 hg38.150200.bed.split13108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13109 0 1 2 100 hg38.150200.bed.split13109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1311 0 1 2 100 hg38.150200.bed.split1311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13110 0 1 2 100 hg38.150200.bed.split13110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13111 0 1 2 100 hg38.150200.bed.split13111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13112 0 1 2 100 hg38.150200.bed.split13112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13113 0 1 2 100 hg38.150200.bed.split13113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13114 0 1 2 100 hg38.150200.bed.split13114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13115 0 1 2 100 hg38.150200.bed.split13115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13116 0 1 2 100 hg38.150200.bed.split13116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13117 0 1 2 100 hg38.150200.bed.split13117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13118 0 1 2 100 hg38.150200.bed.split13118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13119 0 1 2 100 hg38.150200.bed.split13119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1312 0 1 2 100 hg38.150200.bed.split1312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13120 0 1 2 100 hg38.150200.bed.split13120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13121 0 1 2 100 hg38.150200.bed.split13121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13122 0 1 2 100 hg38.150200.bed.split13122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13123 0 1 2 100 hg38.150200.bed.split13123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13124 0 1 2 100 hg38.150200.bed.split13124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13125 0 1 2 100 hg38.150200.bed.split13125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13126 0 1 2 100 hg38.150200.bed.split13126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13127 0 1 2 100 hg38.150200.bed.split13127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13128 0 1 2 100 hg38.150200.bed.split13128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13129 0 1 2 100 hg38.150200.bed.split13129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1313 0 1 2 100 hg38.150200.bed.split1313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13130 0 1 2 100 hg38.150200.bed.split13130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13131 0 1 2 100 hg38.150200.bed.split13131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13132 0 1 2 100 hg38.150200.bed.split13132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13133 0 1 2 100 hg38.150200.bed.split13133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13134 0 1 2 100 hg38.150200.bed.split13134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13135 0 1 2 100 hg38.150200.bed.split13135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13136 0 1 2 100 hg38.150200.bed.split13136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13137 0 1 2 100 hg38.150200.bed.split13137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13138 0 1 2 100 hg38.150200.bed.split13138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13139 0 1 2 100 hg38.150200.bed.split13139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1314 0 1 2 100 hg38.150200.bed.split1314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13140 0 1 2 100 hg38.150200.bed.split13140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13141 0 1 2 100 hg38.150200.bed.split13141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13142 0 1 2 100 hg38.150200.bed.split13142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13143 0 1 2 100 hg38.150200.bed.split13143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13144 0 1 2 100 hg38.150200.bed.split13144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13145 0 1 2 100 hg38.150200.bed.split13145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13146 0 1 2 100 hg38.150200.bed.split13146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13147 0 1 2 100 hg38.150200.bed.split13147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13148 0 1 2 100 hg38.150200.bed.split13148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13149 0 1 2 100 hg38.150200.bed.split13149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1315 0 1 2 100 hg38.150200.bed.split1315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13150 0 1 2 100 hg38.150200.bed.split13150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13151 0 1 2 100 hg38.150200.bed.split13151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13152 0 1 2 100 hg38.150200.bed.split13152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13153 0 1 2 100 hg38.150200.bed.split13153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13154 0 1 2 100 hg38.150200.bed.split13154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13155 0 1 2 100 hg38.150200.bed.split13155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13156 0 1 2 100 hg38.150200.bed.split13156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13157 0 1 2 100 hg38.150200.bed.split13157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13158 0 1 2 100 hg38.150200.bed.split13158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13159 0 1 2 100 hg38.150200.bed.split13159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1316 0 1 2 100 hg38.150200.bed.split1316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13160 0 1 2 100 hg38.150200.bed.split13160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13161 0 1 2 100 hg38.150200.bed.split13161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13162 0 1 2 100 hg38.150200.bed.split13162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13163 0 1 2 100 hg38.150200.bed.split13163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13164 0 1 2 100 hg38.150200.bed.split13164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13165 0 1 2 100 hg38.150200.bed.split13165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13166 0 1 2 100 hg38.150200.bed.split13166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13167 0 1 2 100 hg38.150200.bed.split13167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13168 0 1 2 100 hg38.150200.bed.split13168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13169 0 1 2 100 hg38.150200.bed.split13169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1317 0 1 2 100 hg38.150200.bed.split1317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13170 0 1 2 100 hg38.150200.bed.split13170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13171 0 1 2 100 hg38.150200.bed.split13171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13172 0 1 2 100 hg38.150200.bed.split13172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13173 0 1 2 100 hg38.150200.bed.split13173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13174 0 1 2 100 hg38.150200.bed.split13174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13175 0 1 2 100 hg38.150200.bed.split13175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13176 0 1 2 100 hg38.150200.bed.split13176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13177 0 1 2 100 hg38.150200.bed.split13177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13178 0 1 2 100 hg38.150200.bed.split13178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13179 0 1 2 100 hg38.150200.bed.split13179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1318 0 1 2 100 hg38.150200.bed.split1318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13180 0 1 2 100 hg38.150200.bed.split13180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13181 0 1 2 100 hg38.150200.bed.split13181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13182 0 1 2 100 hg38.150200.bed.split13182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13183 0 1 2 100 hg38.150200.bed.split13183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13184 0 1 2 100 hg38.150200.bed.split13184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13185 0 1 2 100 hg38.150200.bed.split13185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13186 0 1 2 100 hg38.150200.bed.split13186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13187 0 1 2 100 hg38.150200.bed.split13187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13188 0 1 2 100 hg38.150200.bed.split13188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13189 0 1 2 100 hg38.150200.bed.split13189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1319 0 1 2 100 hg38.150200.bed.split1319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13190 0 1 2 100 hg38.150200.bed.split13190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13191 0 1 2 100 hg38.150200.bed.split13191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13192 0 1 2 100 hg38.150200.bed.split13192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13193 0 1 2 100 hg38.150200.bed.split13193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13194 0 1 2 100 hg38.150200.bed.split13194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13195 0 1 2 100 hg38.150200.bed.split13195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13196 0 1 2 100 hg38.150200.bed.split13196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13197 0 1 2 100 hg38.150200.bed.split13197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13198 0 1 2 100 hg38.150200.bed.split13198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13199 0 1 2 100 hg38.150200.bed.split13199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split132 0 1 2 100 hg38.150200.bed.split132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1320 0 1 2 100 hg38.150200.bed.split1320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13200 0 1 2 100 hg38.150200.bed.split13200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13201 0 1 2 100 hg38.150200.bed.split13201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13202 0 1 2 100 hg38.150200.bed.split13202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13203 0 1 2 100 hg38.150200.bed.split13203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13204 0 1 2 100 hg38.150200.bed.split13204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13205 0 1 2 100 hg38.150200.bed.split13205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13206 0 1 2 100 hg38.150200.bed.split13206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13207 0 1 2 100 hg38.150200.bed.split13207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13208 0 1 2 100 hg38.150200.bed.split13208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13209 0 1 2 100 hg38.150200.bed.split13209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1321 0 1 2 100 hg38.150200.bed.split1321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13210 0 1 2 100 hg38.150200.bed.split13210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13211 0 1 2 100 hg38.150200.bed.split13211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13212 0 1 2 100 hg38.150200.bed.split13212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13213 0 1 2 100 hg38.150200.bed.split13213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13214 0 1 2 100 hg38.150200.bed.split13214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13215 0 1 2 100 hg38.150200.bed.split13215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13216 0 1 2 100 hg38.150200.bed.split13216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13217 0 1 2 100 hg38.150200.bed.split13217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13218 0 1 2 100 hg38.150200.bed.split13218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13219 0 1 2 100 hg38.150200.bed.split13219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1322 0 1 2 100 hg38.150200.bed.split1322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13220 0 1 2 100 hg38.150200.bed.split13220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13221 0 1 2 100 hg38.150200.bed.split13221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13222 0 1 2 100 hg38.150200.bed.split13222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13223 0 1 2 100 hg38.150200.bed.split13223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13224 0 1 2 100 hg38.150200.bed.split13224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13225 0 1 2 100 hg38.150200.bed.split13225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13226 0 1 2 100 hg38.150200.bed.split13226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13227 0 1 2 100 hg38.150200.bed.split13227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13228 0 1 2 100 hg38.150200.bed.split13228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13229 0 1 2 100 hg38.150200.bed.split13229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1323 0 1 2 100 hg38.150200.bed.split1323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13230 0 1 2 100 hg38.150200.bed.split13230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13231 0 1 2 100 hg38.150200.bed.split13231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13232 0 1 2 100 hg38.150200.bed.split13232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13233 0 1 2 100 hg38.150200.bed.split13233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13234 0 1 2 100 hg38.150200.bed.split13234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13235 0 1 2 100 hg38.150200.bed.split13235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13236 0 1 2 100 hg38.150200.bed.split13236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13237 0 1 2 100 hg38.150200.bed.split13237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13238 0 1 2 100 hg38.150200.bed.split13238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13239 0 1 2 100 hg38.150200.bed.split13239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1324 0 1 2 100 hg38.150200.bed.split1324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13240 0 1 2 100 hg38.150200.bed.split13240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13241 0 1 2 100 hg38.150200.bed.split13241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13242 0 1 2 100 hg38.150200.bed.split13242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13243 0 1 2 100 hg38.150200.bed.split13243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13244 0 1 2 100 hg38.150200.bed.split13244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13245 0 1 2 100 hg38.150200.bed.split13245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13246 0 1 2 100 hg38.150200.bed.split13246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13247 0 1 2 100 hg38.150200.bed.split13247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13248 0 1 2 100 hg38.150200.bed.split13248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13249 0 1 2 100 hg38.150200.bed.split13249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1325 0 1 2 100 hg38.150200.bed.split1325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13250 0 1 2 100 hg38.150200.bed.split13250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13251 0 1 2 100 hg38.150200.bed.split13251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13252 0 1 2 100 hg38.150200.bed.split13252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13253 0 1 2 100 hg38.150200.bed.split13253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13254 0 1 2 100 hg38.150200.bed.split13254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13255 0 1 2 100 hg38.150200.bed.split13255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13256 0 1 2 100 hg38.150200.bed.split13256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13257 0 1 2 100 hg38.150200.bed.split13257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13258 0 1 2 100 hg38.150200.bed.split13258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13259 0 1 2 100 hg38.150200.bed.split13259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1326 0 1 2 100 hg38.150200.bed.split1326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13260 0 1 2 100 hg38.150200.bed.split13260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13261 0 1 2 100 hg38.150200.bed.split13261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13262 0 1 2 100 hg38.150200.bed.split13262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13263 0 1 2 100 hg38.150200.bed.split13263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13264 0 1 2 100 hg38.150200.bed.split13264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13265 0 1 2 100 hg38.150200.bed.split13265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13266 0 1 2 100 hg38.150200.bed.split13266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13267 0 1 2 100 hg38.150200.bed.split13267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13268 0 1 2 100 hg38.150200.bed.split13268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13269 0 1 2 100 hg38.150200.bed.split13269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1327 0 1 2 100 hg38.150200.bed.split1327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13270 0 1 2 100 hg38.150200.bed.split13270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13271 0 1 2 100 hg38.150200.bed.split13271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13272 0 1 2 100 hg38.150200.bed.split13272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13273 0 1 2 100 hg38.150200.bed.split13273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13274 0 1 2 100 hg38.150200.bed.split13274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13275 0 1 2 100 hg38.150200.bed.split13275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13276 0 1 2 100 hg38.150200.bed.split13276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13277 0 1 2 100 hg38.150200.bed.split13277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13278 0 1 2 100 hg38.150200.bed.split13278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13279 0 1 2 100 hg38.150200.bed.split13279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1328 0 1 2 100 hg38.150200.bed.split1328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13280 0 1 2 100 hg38.150200.bed.split13280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13281 0 1 2 100 hg38.150200.bed.split13281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13282 0 1 2 100 hg38.150200.bed.split13282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13283 0 1 2 100 hg38.150200.bed.split13283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13284 0 1 2 100 hg38.150200.bed.split13284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13285 0 1 2 100 hg38.150200.bed.split13285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13286 0 1 2 100 hg38.150200.bed.split13286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13287 0 1 2 100 hg38.150200.bed.split13287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13288 0 1 2 100 hg38.150200.bed.split13288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13289 0 1 2 100 hg38.150200.bed.split13289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1329 0 1 2 100 hg38.150200.bed.split1329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13290 0 1 2 100 hg38.150200.bed.split13290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13291 0 1 2 100 hg38.150200.bed.split13291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13292 0 1 2 100 hg38.150200.bed.split13292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13293 0 1 2 100 hg38.150200.bed.split13293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13294 0 1 2 100 hg38.150200.bed.split13294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13295 0 1 2 100 hg38.150200.bed.split13295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13296 0 1 2 100 hg38.150200.bed.split13296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13297 0 1 2 100 hg38.150200.bed.split13297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13298 0 1 2 100 hg38.150200.bed.split13298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13299 0 1 2 100 hg38.150200.bed.split13299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split133 0 1 2 100 hg38.150200.bed.split133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1330 0 1 2 100 hg38.150200.bed.split1330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13300 0 1 2 100 hg38.150200.bed.split13300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13301 0 1 2 100 hg38.150200.bed.split13301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13302 0 1 2 100 hg38.150200.bed.split13302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13303 0 1 2 100 hg38.150200.bed.split13303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13304 0 1 2 100 hg38.150200.bed.split13304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13305 0 1 2 100 hg38.150200.bed.split13305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13306 0 1 2 100 hg38.150200.bed.split13306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13307 0 1 2 100 hg38.150200.bed.split13307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13308 0 1 2 100 hg38.150200.bed.split13308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13309 0 1 2 100 hg38.150200.bed.split13309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1331 0 1 2 100 hg38.150200.bed.split1331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13310 0 1 2 100 hg38.150200.bed.split13310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13311 0 1 2 100 hg38.150200.bed.split13311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13312 0 1 2 100 hg38.150200.bed.split13312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13313 0 1 2 100 hg38.150200.bed.split13313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13314 0 1 2 100 hg38.150200.bed.split13314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13315 0 1 2 100 hg38.150200.bed.split13315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13316 0 1 2 100 hg38.150200.bed.split13316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13317 0 1 2 100 hg38.150200.bed.split13317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13318 0 1 2 100 hg38.150200.bed.split13318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13319 0 1 2 100 hg38.150200.bed.split13319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1332 0 1 2 100 hg38.150200.bed.split1332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13320 0 1 2 100 hg38.150200.bed.split13320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13321 0 1 2 100 hg38.150200.bed.split13321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13322 0 1 2 100 hg38.150200.bed.split13322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13323 0 1 2 100 hg38.150200.bed.split13323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13324 0 1 2 100 hg38.150200.bed.split13324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13325 0 1 2 100 hg38.150200.bed.split13325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13326 0 1 2 100 hg38.150200.bed.split13326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13327 0 1 2 100 hg38.150200.bed.split13327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13328 0 1 2 100 hg38.150200.bed.split13328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13329 0 1 2 100 hg38.150200.bed.split13329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1333 0 1 2 100 hg38.150200.bed.split1333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13330 0 1 2 100 hg38.150200.bed.split13330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13331 0 1 2 100 hg38.150200.bed.split13331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13332 0 1 2 100 hg38.150200.bed.split13332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13333 0 1 2 100 hg38.150200.bed.split13333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13334 0 1 2 100 hg38.150200.bed.split13334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13335 0 1 2 100 hg38.150200.bed.split13335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13336 0 1 2 100 hg38.150200.bed.split13336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13337 0 1 2 100 hg38.150200.bed.split13337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13338 0 1 2 100 hg38.150200.bed.split13338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13339 0 1 2 100 hg38.150200.bed.split13339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1334 0 1 2 100 hg38.150200.bed.split1334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13340 0 1 2 100 hg38.150200.bed.split13340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13341 0 1 2 100 hg38.150200.bed.split13341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13342 0 1 2 100 hg38.150200.bed.split13342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13343 0 1 2 100 hg38.150200.bed.split13343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13344 0 1 2 100 hg38.150200.bed.split13344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13345 0 1 2 100 hg38.150200.bed.split13345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13346 0 1 2 100 hg38.150200.bed.split13346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13347 0 1 2 100 hg38.150200.bed.split13347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13348 0 1 2 100 hg38.150200.bed.split13348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13349 0 1 2 100 hg38.150200.bed.split13349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1335 0 1 2 100 hg38.150200.bed.split1335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13350 0 1 2 100 hg38.150200.bed.split13350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13351 0 1 2 100 hg38.150200.bed.split13351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13352 0 1 2 100 hg38.150200.bed.split13352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13353 0 1 2 100 hg38.150200.bed.split13353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13354 0 1 2 100 hg38.150200.bed.split13354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13355 0 1 2 100 hg38.150200.bed.split13355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13356 0 1 2 100 hg38.150200.bed.split13356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13357 0 1 2 100 hg38.150200.bed.split13357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13358 0 1 2 100 hg38.150200.bed.split13358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13359 0 1 2 100 hg38.150200.bed.split13359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1336 0 1 2 100 hg38.150200.bed.split1336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13360 0 1 2 100 hg38.150200.bed.split13360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13361 0 1 2 100 hg38.150200.bed.split13361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13362 0 1 2 100 hg38.150200.bed.split13362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13363 0 1 2 100 hg38.150200.bed.split13363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13364 0 1 2 100 hg38.150200.bed.split13364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13365 0 1 2 100 hg38.150200.bed.split13365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13366 0 1 2 100 hg38.150200.bed.split13366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13367 0 1 2 100 hg38.150200.bed.split13367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13368 0 1 2 100 hg38.150200.bed.split13368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13369 0 1 2 100 hg38.150200.bed.split13369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1337 0 1 2 100 hg38.150200.bed.split1337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13370 0 1 2 100 hg38.150200.bed.split13370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13371 0 1 2 100 hg38.150200.bed.split13371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13372 0 1 2 100 hg38.150200.bed.split13372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13373 0 1 2 100 hg38.150200.bed.split13373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13374 0 1 2 100 hg38.150200.bed.split13374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13375 0 1 2 100 hg38.150200.bed.split13375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13376 0 1 2 100 hg38.150200.bed.split13376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13377 0 1 2 100 hg38.150200.bed.split13377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13378 0 1 2 100 hg38.150200.bed.split13378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13379 0 1 2 100 hg38.150200.bed.split13379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1338 0 1 2 100 hg38.150200.bed.split1338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13380 0 1 2 100 hg38.150200.bed.split13380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13381 0 1 2 100 hg38.150200.bed.split13381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13382 0 1 2 100 hg38.150200.bed.split13382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13383 0 1 2 100 hg38.150200.bed.split13383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13384 0 1 2 100 hg38.150200.bed.split13384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13385 0 1 2 100 hg38.150200.bed.split13385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13386 0 1 2 100 hg38.150200.bed.split13386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13387 0 1 2 100 hg38.150200.bed.split13387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13388 0 1 2 100 hg38.150200.bed.split13388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13389 0 1 2 100 hg38.150200.bed.split13389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1339 0 1 2 100 hg38.150200.bed.split1339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13390 0 1 2 100 hg38.150200.bed.split13390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13391 0 1 2 100 hg38.150200.bed.split13391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13392 0 1 2 100 hg38.150200.bed.split13392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13393 0 1 2 100 hg38.150200.bed.split13393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13394 0 1 2 100 hg38.150200.bed.split13394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13395 0 1 2 100 hg38.150200.bed.split13395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13396 0 1 2 100 hg38.150200.bed.split13396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13397 0 1 2 100 hg38.150200.bed.split13397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13398 0 1 2 100 hg38.150200.bed.split13398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13399 0 1 2 100 hg38.150200.bed.split13399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split134 0 1 2 100 hg38.150200.bed.split134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1340 0 1 2 100 hg38.150200.bed.split1340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13400 0 1 2 100 hg38.150200.bed.split13400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13401 0 1 2 100 hg38.150200.bed.split13401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13402 0 1 2 100 hg38.150200.bed.split13402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13403 0 1 2 100 hg38.150200.bed.split13403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13404 0 1 2 100 hg38.150200.bed.split13404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13405 0 1 2 100 hg38.150200.bed.split13405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13406 0 1 2 100 hg38.150200.bed.split13406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13407 0 1 2 100 hg38.150200.bed.split13407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13408 0 1 2 100 hg38.150200.bed.split13408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13409 0 1 2 100 hg38.150200.bed.split13409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1341 0 1 2 100 hg38.150200.bed.split1341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13410 0 1 2 100 hg38.150200.bed.split13410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13411 0 1 2 100 hg38.150200.bed.split13411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13412 0 1 2 100 hg38.150200.bed.split13412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13413 0 1 2 100 hg38.150200.bed.split13413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13414 0 1 2 100 hg38.150200.bed.split13414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13415 0 1 2 100 hg38.150200.bed.split13415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13416 0 1 2 100 hg38.150200.bed.split13416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13417 0 1 2 100 hg38.150200.bed.split13417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13418 0 1 2 100 hg38.150200.bed.split13418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13419 0 1 2 100 hg38.150200.bed.split13419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1342 0 1 2 100 hg38.150200.bed.split1342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13420 0 1 2 100 hg38.150200.bed.split13420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13421 0 1 2 100 hg38.150200.bed.split13421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13422 0 1 2 100 hg38.150200.bed.split13422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13423 0 1 2 100 hg38.150200.bed.split13423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13424 0 1 2 100 hg38.150200.bed.split13424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13425 0 1 2 100 hg38.150200.bed.split13425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13426 0 1 2 100 hg38.150200.bed.split13426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13427 0 1 2 100 hg38.150200.bed.split13427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13428 0 1 2 100 hg38.150200.bed.split13428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13429 0 1 2 100 hg38.150200.bed.split13429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1343 0 1 2 100 hg38.150200.bed.split1343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13430 0 1 2 100 hg38.150200.bed.split13430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13431 0 1 2 100 hg38.150200.bed.split13431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13432 0 1 2 100 hg38.150200.bed.split13432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13433 0 1 2 100 hg38.150200.bed.split13433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13434 0 1 2 100 hg38.150200.bed.split13434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13435 0 1 2 100 hg38.150200.bed.split13435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13436 0 1 2 100 hg38.150200.bed.split13436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13437 0 1 2 100 hg38.150200.bed.split13437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13438 0 1 2 100 hg38.150200.bed.split13438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13439 0 1 2 100 hg38.150200.bed.split13439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1344 0 1 2 100 hg38.150200.bed.split1344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13440 0 1 2 100 hg38.150200.bed.split13440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13441 0 1 2 100 hg38.150200.bed.split13441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13442 0 1 2 100 hg38.150200.bed.split13442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13443 0 1 2 100 hg38.150200.bed.split13443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13444 0 1 2 100 hg38.150200.bed.split13444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13445 0 1 2 100 hg38.150200.bed.split13445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13446 0 1 2 100 hg38.150200.bed.split13446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13447 0 1 2 100 hg38.150200.bed.split13447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13448 0 1 2 100 hg38.150200.bed.split13448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13449 0 1 2 100 hg38.150200.bed.split13449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1345 0 1 2 100 hg38.150200.bed.split1345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13450 0 1 2 100 hg38.150200.bed.split13450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13451 0 1 2 100 hg38.150200.bed.split13451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13452 0 1 2 100 hg38.150200.bed.split13452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13453 0 1 2 100 hg38.150200.bed.split13453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13454 0 1 2 100 hg38.150200.bed.split13454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13455 0 1 2 100 hg38.150200.bed.split13455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13456 0 1 2 100 hg38.150200.bed.split13456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13457 0 1 2 100 hg38.150200.bed.split13457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13458 0 1 2 100 hg38.150200.bed.split13458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13459 0 1 2 100 hg38.150200.bed.split13459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1346 0 1 2 100 hg38.150200.bed.split1346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13460 0 1 2 100 hg38.150200.bed.split13460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13461 0 1 2 100 hg38.150200.bed.split13461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13462 0 1 2 100 hg38.150200.bed.split13462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13463 0 1 2 100 hg38.150200.bed.split13463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13464 0 1 2 100 hg38.150200.bed.split13464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13465 0 1 2 100 hg38.150200.bed.split13465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13466 0 1 2 100 hg38.150200.bed.split13466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13467 0 1 2 100 hg38.150200.bed.split13467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13468 0 1 2 100 hg38.150200.bed.split13468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13469 0 1 2 100 hg38.150200.bed.split13469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1347 0 1 2 100 hg38.150200.bed.split1347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13470 0 1 2 100 hg38.150200.bed.split13470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13471 0 1 2 100 hg38.150200.bed.split13471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13472 0 1 2 100 hg38.150200.bed.split13472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13473 0 1 2 100 hg38.150200.bed.split13473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13474 0 1 2 100 hg38.150200.bed.split13474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13475 0 1 2 100 hg38.150200.bed.split13475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13476 0 1 2 100 hg38.150200.bed.split13476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13477 0 1 2 100 hg38.150200.bed.split13477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13478 0 1 2 100 hg38.150200.bed.split13478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13479 0 1 2 100 hg38.150200.bed.split13479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1348 0 1 2 100 hg38.150200.bed.split1348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13480 0 1 2 100 hg38.150200.bed.split13480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13481 0 1 2 100 hg38.150200.bed.split13481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13482 0 1 2 100 hg38.150200.bed.split13482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13483 0 1 2 100 hg38.150200.bed.split13483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13484 0 1 2 100 hg38.150200.bed.split13484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13485 0 1 2 100 hg38.150200.bed.split13485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13486 0 1 2 100 hg38.150200.bed.split13486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13487 0 1 2 100 hg38.150200.bed.split13487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13488 0 1 2 100 hg38.150200.bed.split13488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13489 0 1 2 100 hg38.150200.bed.split13489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1349 0 1 2 100 hg38.150200.bed.split1349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13490 0 1 2 100 hg38.150200.bed.split13490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13491 0 1 2 100 hg38.150200.bed.split13491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13492 0 1 2 100 hg38.150200.bed.split13492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13493 0 1 2 100 hg38.150200.bed.split13493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13494 0 1 2 100 hg38.150200.bed.split13494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13495 0 1 2 100 hg38.150200.bed.split13495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13496 0 1 2 100 hg38.150200.bed.split13496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13497 0 1 2 100 hg38.150200.bed.split13497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13498 0 1 2 100 hg38.150200.bed.split13498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13499 0 1 2 100 hg38.150200.bed.split13499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split135 0 1 2 100 hg38.150200.bed.split135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1350 0 1 2 100 hg38.150200.bed.split1350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13500 0 1 2 100 hg38.150200.bed.split13500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13501 0 1 2 100 hg38.150200.bed.split13501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13502 0 1 2 100 hg38.150200.bed.split13502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13503 0 1 2 100 hg38.150200.bed.split13503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13504 0 1 2 100 hg38.150200.bed.split13504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13505 0 1 2 100 hg38.150200.bed.split13505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13506 0 1 2 100 hg38.150200.bed.split13506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13507 0 1 2 100 hg38.150200.bed.split13507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13508 0 1 2 100 hg38.150200.bed.split13508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13509 0 1 2 100 hg38.150200.bed.split13509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1351 0 1 2 100 hg38.150200.bed.split1351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13510 0 1 2 100 hg38.150200.bed.split13510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13511 0 1 2 100 hg38.150200.bed.split13511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13512 0 1 2 100 hg38.150200.bed.split13512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13513 0 1 2 100 hg38.150200.bed.split13513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13514 0 1 2 100 hg38.150200.bed.split13514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13515 0 1 2 100 hg38.150200.bed.split13515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13516 0 1 2 100 hg38.150200.bed.split13516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13517 0 1 2 100 hg38.150200.bed.split13517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13518 0 1 2 100 hg38.150200.bed.split13518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13519 0 1 2 100 hg38.150200.bed.split13519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1352 0 1 2 100 hg38.150200.bed.split1352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13520 0 1 2 100 hg38.150200.bed.split13520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13521 0 1 2 100 hg38.150200.bed.split13521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13522 0 1 2 100 hg38.150200.bed.split13522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13523 0 1 2 100 hg38.150200.bed.split13523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13524 0 1 2 100 hg38.150200.bed.split13524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13525 0 1 2 100 hg38.150200.bed.split13525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13526 0 1 2 100 hg38.150200.bed.split13526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13527 0 1 2 100 hg38.150200.bed.split13527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13528 0 1 2 100 hg38.150200.bed.split13528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13529 0 1 2 100 hg38.150200.bed.split13529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1353 0 1 2 100 hg38.150200.bed.split1353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13530 0 1 2 100 hg38.150200.bed.split13530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13531 0 1 2 100 hg38.150200.bed.split13531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13532 0 1 2 100 hg38.150200.bed.split13532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13533 0 1 2 100 hg38.150200.bed.split13533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13534 0 1 2 100 hg38.150200.bed.split13534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13535 0 1 2 100 hg38.150200.bed.split13535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13536 0 1 2 100 hg38.150200.bed.split13536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13537 0 1 2 100 hg38.150200.bed.split13537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13538 0 1 2 100 hg38.150200.bed.split13538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13539 0 1 2 100 hg38.150200.bed.split13539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1354 0 1 2 100 hg38.150200.bed.split1354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13540 0 1 2 100 hg38.150200.bed.split13540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13541 0 1 2 100 hg38.150200.bed.split13541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13542 0 1 2 100 hg38.150200.bed.split13542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13543 0 1 2 100 hg38.150200.bed.split13543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13544 0 1 2 100 hg38.150200.bed.split13544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13545 0 1 2 100 hg38.150200.bed.split13545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13546 0 1 2 100 hg38.150200.bed.split13546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13547 0 1 2 100 hg38.150200.bed.split13547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13548 0 1 2 100 hg38.150200.bed.split13548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13549 0 1 2 100 hg38.150200.bed.split13549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1355 0 1 2 100 hg38.150200.bed.split1355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13550 0 1 2 100 hg38.150200.bed.split13550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13551 0 1 2 100 hg38.150200.bed.split13551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13552 0 1 2 100 hg38.150200.bed.split13552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13553 0 1 2 100 hg38.150200.bed.split13553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13554 0 1 2 100 hg38.150200.bed.split13554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13555 0 1 2 100 hg38.150200.bed.split13555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13556 0 1 2 100 hg38.150200.bed.split13556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13557 0 1 2 100 hg38.150200.bed.split13557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13558 0 1 2 100 hg38.150200.bed.split13558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13559 0 1 2 100 hg38.150200.bed.split13559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1356 0 1 2 100 hg38.150200.bed.split1356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13560 0 1 2 100 hg38.150200.bed.split13560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13561 0 1 2 100 hg38.150200.bed.split13561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13562 0 1 2 100 hg38.150200.bed.split13562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13563 0 1 2 100 hg38.150200.bed.split13563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13564 0 1 2 100 hg38.150200.bed.split13564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13565 0 1 2 100 hg38.150200.bed.split13565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13566 0 1 2 100 hg38.150200.bed.split13566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13567 0 1 2 100 hg38.150200.bed.split13567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13568 0 1 2 100 hg38.150200.bed.split13568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13569 0 1 2 100 hg38.150200.bed.split13569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1357 0 1 2 100 hg38.150200.bed.split1357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13570 0 1 2 100 hg38.150200.bed.split13570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13571 0 1 2 100 hg38.150200.bed.split13571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13572 0 1 2 100 hg38.150200.bed.split13572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13573 0 1 2 100 hg38.150200.bed.split13573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13574 0 1 2 100 hg38.150200.bed.split13574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13575 0 1 2 100 hg38.150200.bed.split13575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13576 0 1 2 100 hg38.150200.bed.split13576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13577 0 1 2 100 hg38.150200.bed.split13577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13578 0 1 2 100 hg38.150200.bed.split13578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13579 0 1 2 100 hg38.150200.bed.split13579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1358 0 1 2 100 hg38.150200.bed.split1358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13580 0 1 2 100 hg38.150200.bed.split13580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13581 0 1 2 100 hg38.150200.bed.split13581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13582 0 1 2 100 hg38.150200.bed.split13582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13583 0 1 2 100 hg38.150200.bed.split13583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13584 0 1 2 100 hg38.150200.bed.split13584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13585 0 1 2 100 hg38.150200.bed.split13585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13586 0 1 2 100 hg38.150200.bed.split13586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13587 0 1 2 100 hg38.150200.bed.split13587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13588 0 1 2 100 hg38.150200.bed.split13588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13589 0 1 2 100 hg38.150200.bed.split13589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1359 0 1 2 100 hg38.150200.bed.split1359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13590 0 1 2 100 hg38.150200.bed.split13590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13591 0 1 2 100 hg38.150200.bed.split13591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13592 0 1 2 100 hg38.150200.bed.split13592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13593 0 1 2 100 hg38.150200.bed.split13593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13594 0 1 2 100 hg38.150200.bed.split13594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13595 0 1 2 100 hg38.150200.bed.split13595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13596 0 1 2 100 hg38.150200.bed.split13596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13597 0 1 2 100 hg38.150200.bed.split13597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13598 0 1 2 100 hg38.150200.bed.split13598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13599 0 1 2 100 hg38.150200.bed.split13599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split136 0 1 2 100 hg38.150200.bed.split136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1360 0 1 2 100 hg38.150200.bed.split1360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13600 0 1 2 100 hg38.150200.bed.split13600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13601 0 1 2 100 hg38.150200.bed.split13601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13602 0 1 2 100 hg38.150200.bed.split13602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13603 0 1 2 100 hg38.150200.bed.split13603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13604 0 1 2 100 hg38.150200.bed.split13604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13605 0 1 2 100 hg38.150200.bed.split13605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13606 0 1 2 100 hg38.150200.bed.split13606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13607 0 1 2 100 hg38.150200.bed.split13607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13608 0 1 2 100 hg38.150200.bed.split13608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13609 0 1 2 100 hg38.150200.bed.split13609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1361 0 1 2 100 hg38.150200.bed.split1361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13610 0 1 2 100 hg38.150200.bed.split13610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13611 0 1 2 100 hg38.150200.bed.split13611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13612 0 1 2 100 hg38.150200.bed.split13612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13613 0 1 2 100 hg38.150200.bed.split13613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13614 0 1 2 100 hg38.150200.bed.split13614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13615 0 1 2 100 hg38.150200.bed.split13615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13616 0 1 2 100 hg38.150200.bed.split13616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13617 0 1 2 100 hg38.150200.bed.split13617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13618 0 1 2 100 hg38.150200.bed.split13618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13619 0 1 2 100 hg38.150200.bed.split13619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1362 0 1 2 100 hg38.150200.bed.split1362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13620 0 1 2 100 hg38.150200.bed.split13620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13621 0 1 2 100 hg38.150200.bed.split13621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13622 0 1 2 100 hg38.150200.bed.split13622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13623 0 1 2 100 hg38.150200.bed.split13623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13624 0 1 2 100 hg38.150200.bed.split13624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13625 0 1 2 100 hg38.150200.bed.split13625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13626 0 1 2 100 hg38.150200.bed.split13626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13627 0 1 2 100 hg38.150200.bed.split13627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13628 0 1 2 100 hg38.150200.bed.split13628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13629 0 1 2 100 hg38.150200.bed.split13629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1363 0 1 2 100 hg38.150200.bed.split1363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13630 0 1 2 100 hg38.150200.bed.split13630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13631 0 1 2 100 hg38.150200.bed.split13631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13632 0 1 2 100 hg38.150200.bed.split13632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13633 0 1 2 100 hg38.150200.bed.split13633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13634 0 1 2 100 hg38.150200.bed.split13634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13635 0 1 2 100 hg38.150200.bed.split13635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13636 0 1 2 100 hg38.150200.bed.split13636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13637 0 1 2 100 hg38.150200.bed.split13637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13638 0 1 2 100 hg38.150200.bed.split13638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13639 0 1 2 100 hg38.150200.bed.split13639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1364 0 1 2 100 hg38.150200.bed.split1364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13640 0 1 2 100 hg38.150200.bed.split13640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13641 0 1 2 100 hg38.150200.bed.split13641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13642 0 1 2 100 hg38.150200.bed.split13642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13643 0 1 2 100 hg38.150200.bed.split13643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13644 0 1 2 100 hg38.150200.bed.split13644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13645 0 1 2 100 hg38.150200.bed.split13645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13646 0 1 2 100 hg38.150200.bed.split13646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13647 0 1 2 100 hg38.150200.bed.split13647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13648 0 1 2 100 hg38.150200.bed.split13648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13649 0 1 2 100 hg38.150200.bed.split13649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1365 0 1 2 100 hg38.150200.bed.split1365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13650 0 1 2 100 hg38.150200.bed.split13650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13651 0 1 2 100 hg38.150200.bed.split13651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13652 0 1 2 100 hg38.150200.bed.split13652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13653 0 1 2 100 hg38.150200.bed.split13653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13654 0 1 2 100 hg38.150200.bed.split13654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13655 0 1 2 100 hg38.150200.bed.split13655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13656 0 1 2 100 hg38.150200.bed.split13656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13657 0 1 2 100 hg38.150200.bed.split13657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13658 0 1 2 100 hg38.150200.bed.split13658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13659 0 1 2 100 hg38.150200.bed.split13659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1366 0 1 2 100 hg38.150200.bed.split1366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13660 0 1 2 100 hg38.150200.bed.split13660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13661 0 1 2 100 hg38.150200.bed.split13661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13662 0 1 2 100 hg38.150200.bed.split13662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13663 0 1 2 100 hg38.150200.bed.split13663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13664 0 1 2 100 hg38.150200.bed.split13664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13665 0 1 2 100 hg38.150200.bed.split13665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13666 0 1 2 100 hg38.150200.bed.split13666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13667 0 1 2 100 hg38.150200.bed.split13667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13668 0 1 2 100 hg38.150200.bed.split13668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13669 0 1 2 100 hg38.150200.bed.split13669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1367 0 1 2 100 hg38.150200.bed.split1367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13670 0 1 2 100 hg38.150200.bed.split13670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13671 0 1 2 100 hg38.150200.bed.split13671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13672 0 1 2 100 hg38.150200.bed.split13672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13673 0 1 2 100 hg38.150200.bed.split13673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13674 0 1 2 100 hg38.150200.bed.split13674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13675 0 1 2 100 hg38.150200.bed.split13675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13676 0 1 2 100 hg38.150200.bed.split13676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13677 0 1 2 100 hg38.150200.bed.split13677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13678 0 1 2 100 hg38.150200.bed.split13678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13679 0 1 2 100 hg38.150200.bed.split13679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1368 0 1 2 100 hg38.150200.bed.split1368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13680 0 1 2 100 hg38.150200.bed.split13680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13681 0 1 2 100 hg38.150200.bed.split13681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13682 0 1 2 100 hg38.150200.bed.split13682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13683 0 1 2 100 hg38.150200.bed.split13683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13684 0 1 2 100 hg38.150200.bed.split13684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13685 0 1 2 100 hg38.150200.bed.split13685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13686 0 1 2 100 hg38.150200.bed.split13686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13687 0 1 2 100 hg38.150200.bed.split13687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13688 0 1 2 100 hg38.150200.bed.split13688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13689 0 1 2 100 hg38.150200.bed.split13689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1369 0 1 2 100 hg38.150200.bed.split1369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13690 0 1 2 100 hg38.150200.bed.split13690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13691 0 1 2 100 hg38.150200.bed.split13691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13692 0 1 2 100 hg38.150200.bed.split13692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13693 0 1 2 100 hg38.150200.bed.split13693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13694 0 1 2 100 hg38.150200.bed.split13694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13695 0 1 2 100 hg38.150200.bed.split13695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13696 0 1 2 100 hg38.150200.bed.split13696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13697 0 1 2 100 hg38.150200.bed.split13697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13698 0 1 2 100 hg38.150200.bed.split13698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13699 0 1 2 100 hg38.150200.bed.split13699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split137 0 1 2 100 hg38.150200.bed.split137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1370 0 1 2 100 hg38.150200.bed.split1370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13700 0 1 2 100 hg38.150200.bed.split13700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13701 0 1 2 100 hg38.150200.bed.split13701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13702 0 1 2 100 hg38.150200.bed.split13702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13703 0 1 2 100 hg38.150200.bed.split13703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13704 0 1 2 100 hg38.150200.bed.split13704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13705 0 1 2 100 hg38.150200.bed.split13705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13706 0 1 2 100 hg38.150200.bed.split13706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13707 0 1 2 100 hg38.150200.bed.split13707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13708 0 1 2 100 hg38.150200.bed.split13708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13709 0 1 2 100 hg38.150200.bed.split13709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1371 0 1 2 100 hg38.150200.bed.split1371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13710 0 1 2 100 hg38.150200.bed.split13710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13711 0 1 2 100 hg38.150200.bed.split13711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13712 0 1 2 100 hg38.150200.bed.split13712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13713 0 1 2 100 hg38.150200.bed.split13713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13714 0 1 2 100 hg38.150200.bed.split13714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13715 0 1 2 100 hg38.150200.bed.split13715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13716 0 1 2 100 hg38.150200.bed.split13716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13717 0 1 2 100 hg38.150200.bed.split13717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13718 0 1 2 100 hg38.150200.bed.split13718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13719 0 1 2 100 hg38.150200.bed.split13719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1372 0 1 2 100 hg38.150200.bed.split1372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13720 0 1 2 100 hg38.150200.bed.split13720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13721 0 1 2 100 hg38.150200.bed.split13721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13722 0 1 2 100 hg38.150200.bed.split13722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13723 0 1 2 100 hg38.150200.bed.split13723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13724 0 1 2 100 hg38.150200.bed.split13724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13725 0 1 2 100 hg38.150200.bed.split13725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13726 0 1 2 100 hg38.150200.bed.split13726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13727 0 1 2 100 hg38.150200.bed.split13727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13728 0 1 2 100 hg38.150200.bed.split13728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13729 0 1 2 100 hg38.150200.bed.split13729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1373 0 1 2 100 hg38.150200.bed.split1373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13730 0 1 2 100 hg38.150200.bed.split13730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13731 0 1 2 100 hg38.150200.bed.split13731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13732 0 1 2 100 hg38.150200.bed.split13732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13733 0 1 2 100 hg38.150200.bed.split13733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13734 0 1 2 100 hg38.150200.bed.split13734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13735 0 1 2 100 hg38.150200.bed.split13735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13736 0 1 2 100 hg38.150200.bed.split13736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13737 0 1 2 100 hg38.150200.bed.split13737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13738 0 1 2 100 hg38.150200.bed.split13738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13739 0 1 2 100 hg38.150200.bed.split13739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1374 0 1 2 100 hg38.150200.bed.split1374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13740 0 1 2 100 hg38.150200.bed.split13740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13741 0 1 2 100 hg38.150200.bed.split13741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13742 0 1 2 100 hg38.150200.bed.split13742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13743 0 1 2 100 hg38.150200.bed.split13743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13744 0 1 2 100 hg38.150200.bed.split13744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13745 0 1 2 100 hg38.150200.bed.split13745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13746 0 1 2 100 hg38.150200.bed.split13746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13747 0 1 2 100 hg38.150200.bed.split13747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13748 0 1 2 100 hg38.150200.bed.split13748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13749 0 1 2 100 hg38.150200.bed.split13749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1375 0 1 2 100 hg38.150200.bed.split1375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13750 0 1 2 100 hg38.150200.bed.split13750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13751 0 1 2 100 hg38.150200.bed.split13751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13752 0 1 2 100 hg38.150200.bed.split13752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13753 0 1 2 100 hg38.150200.bed.split13753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13754 0 1 2 100 hg38.150200.bed.split13754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13755 0 1 2 100 hg38.150200.bed.split13755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13756 0 1 2 100 hg38.150200.bed.split13756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13757 0 1 2 100 hg38.150200.bed.split13757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13758 0 1 2 100 hg38.150200.bed.split13758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13759 0 1 2 100 hg38.150200.bed.split13759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1376 0 1 2 100 hg38.150200.bed.split1376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13760 0 1 2 100 hg38.150200.bed.split13760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13761 0 1 2 100 hg38.150200.bed.split13761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13762 0 1 2 100 hg38.150200.bed.split13762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13763 0 1 2 100 hg38.150200.bed.split13763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13764 0 1 2 100 hg38.150200.bed.split13764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13765 0 1 2 100 hg38.150200.bed.split13765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13766 0 1 2 100 hg38.150200.bed.split13766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13767 0 1 2 100 hg38.150200.bed.split13767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13768 0 1 2 100 hg38.150200.bed.split13768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13769 0 1 2 100 hg38.150200.bed.split13769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1377 0 1 2 100 hg38.150200.bed.split1377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13770 0 1 2 100 hg38.150200.bed.split13770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13771 0 1 2 100 hg38.150200.bed.split13771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13772 0 1 2 100 hg38.150200.bed.split13772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13773 0 1 2 100 hg38.150200.bed.split13773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13774 0 1 2 100 hg38.150200.bed.split13774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13775 0 1 2 100 hg38.150200.bed.split13775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13776 0 1 2 100 hg38.150200.bed.split13776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13777 0 1 2 100 hg38.150200.bed.split13777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13778 0 1 2 100 hg38.150200.bed.split13778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13779 0 1 2 100 hg38.150200.bed.split13779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1378 0 1 2 100 hg38.150200.bed.split1378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13780 0 1 2 100 hg38.150200.bed.split13780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13781 0 1 2 100 hg38.150200.bed.split13781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13782 0 1 2 100 hg38.150200.bed.split13782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13783 0 1 2 100 hg38.150200.bed.split13783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13784 0 1 2 100 hg38.150200.bed.split13784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13785 0 1 2 100 hg38.150200.bed.split13785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13786 0 1 2 100 hg38.150200.bed.split13786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13787 0 1 2 100 hg38.150200.bed.split13787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13788 0 1 2 100 hg38.150200.bed.split13788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13789 0 1 2 100 hg38.150200.bed.split13789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1379 0 1 2 100 hg38.150200.bed.split1379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13790 0 1 2 100 hg38.150200.bed.split13790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13791 0 1 2 100 hg38.150200.bed.split13791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13792 0 1 2 100 hg38.150200.bed.split13792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13793 0 1 2 100 hg38.150200.bed.split13793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13794 0 1 2 100 hg38.150200.bed.split13794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13795 0 1 2 100 hg38.150200.bed.split13795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13796 0 1 2 100 hg38.150200.bed.split13796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13797 0 1 2 100 hg38.150200.bed.split13797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13798 0 1 2 100 hg38.150200.bed.split13798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13799 0 1 2 100 hg38.150200.bed.split13799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split138 0 1 2 100 hg38.150200.bed.split138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1380 0 1 2 100 hg38.150200.bed.split1380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13800 0 1 2 100 hg38.150200.bed.split13800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13801 0 1 2 100 hg38.150200.bed.split13801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13802 0 1 2 100 hg38.150200.bed.split13802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13803 0 1 2 100 hg38.150200.bed.split13803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13804 0 1 2 100 hg38.150200.bed.split13804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13805 0 1 2 100 hg38.150200.bed.split13805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13806 0 1 2 100 hg38.150200.bed.split13806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13807 0 1 2 100 hg38.150200.bed.split13807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13808 0 1 2 100 hg38.150200.bed.split13808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13809 0 1 2 100 hg38.150200.bed.split13809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1381 0 1 2 100 hg38.150200.bed.split1381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13810 0 1 2 100 hg38.150200.bed.split13810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13811 0 1 2 100 hg38.150200.bed.split13811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13812 0 1 2 100 hg38.150200.bed.split13812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13813 0 1 2 100 hg38.150200.bed.split13813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13814 0 1 2 100 hg38.150200.bed.split13814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13815 0 1 2 100 hg38.150200.bed.split13815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13816 0 1 2 100 hg38.150200.bed.split13816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13817 0 1 2 100 hg38.150200.bed.split13817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13818 0 1 2 100 hg38.150200.bed.split13818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13819 0 1 2 100 hg38.150200.bed.split13819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1382 0 1 2 100 hg38.150200.bed.split1382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13820 0 1 2 100 hg38.150200.bed.split13820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13821 0 1 2 100 hg38.150200.bed.split13821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13822 0 1 2 100 hg38.150200.bed.split13822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13823 0 1 2 100 hg38.150200.bed.split13823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13824 0 1 2 100 hg38.150200.bed.split13824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13825 0 1 2 100 hg38.150200.bed.split13825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13826 0 1 2 100 hg38.150200.bed.split13826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13827 0 1 2 100 hg38.150200.bed.split13827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13828 0 1 2 100 hg38.150200.bed.split13828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13829 0 1 2 100 hg38.150200.bed.split13829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1383 0 1 2 100 hg38.150200.bed.split1383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13830 0 1 2 100 hg38.150200.bed.split13830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13831 0 1 2 100 hg38.150200.bed.split13831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13832 0 1 2 100 hg38.150200.bed.split13832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13833 0 1 2 100 hg38.150200.bed.split13833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13834 0 1 2 100 hg38.150200.bed.split13834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13835 0 1 2 100 hg38.150200.bed.split13835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13836 0 1 2 100 hg38.150200.bed.split13836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13837 0 1 2 100 hg38.150200.bed.split13837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13838 0 1 2 100 hg38.150200.bed.split13838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13839 0 1 2 100 hg38.150200.bed.split13839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1384 0 1 2 100 hg38.150200.bed.split1384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13840 0 1 2 100 hg38.150200.bed.split13840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13841 0 1 2 100 hg38.150200.bed.split13841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13842 0 1 2 100 hg38.150200.bed.split13842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13843 0 1 2 100 hg38.150200.bed.split13843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13844 0 1 2 100 hg38.150200.bed.split13844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13845 0 1 2 100 hg38.150200.bed.split13845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13846 0 1 2 100 hg38.150200.bed.split13846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13847 0 1 2 100 hg38.150200.bed.split13847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13848 0 1 2 100 hg38.150200.bed.split13848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13849 0 1 2 100 hg38.150200.bed.split13849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1385 0 1 2 100 hg38.150200.bed.split1385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13850 0 1 2 100 hg38.150200.bed.split13850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13851 0 1 2 100 hg38.150200.bed.split13851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13852 0 1 2 100 hg38.150200.bed.split13852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13853 0 1 2 100 hg38.150200.bed.split13853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13854 0 1 2 100 hg38.150200.bed.split13854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13855 0 1 2 100 hg38.150200.bed.split13855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13856 0 1 2 100 hg38.150200.bed.split13856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13857 0 1 2 100 hg38.150200.bed.split13857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13858 0 1 2 100 hg38.150200.bed.split13858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13859 0 1 2 100 hg38.150200.bed.split13859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1386 0 1 2 100 hg38.150200.bed.split1386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13860 0 1 2 100 hg38.150200.bed.split13860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13861 0 1 2 100 hg38.150200.bed.split13861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13862 0 1 2 100 hg38.150200.bed.split13862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13863 0 1 2 100 hg38.150200.bed.split13863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13864 0 1 2 100 hg38.150200.bed.split13864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13865 0 1 2 100 hg38.150200.bed.split13865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13866 0 1 2 100 hg38.150200.bed.split13866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13867 0 1 2 100 hg38.150200.bed.split13867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13868 0 1 2 100 hg38.150200.bed.split13868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13869 0 1 2 100 hg38.150200.bed.split13869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1387 0 1 2 100 hg38.150200.bed.split1387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13870 0 1 2 100 hg38.150200.bed.split13870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13871 0 1 2 100 hg38.150200.bed.split13871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13872 0 1 2 100 hg38.150200.bed.split13872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13873 0 1 2 100 hg38.150200.bed.split13873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13874 0 1 2 100 hg38.150200.bed.split13874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13875 0 1 2 100 hg38.150200.bed.split13875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13876 0 1 2 100 hg38.150200.bed.split13876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13877 0 1 2 100 hg38.150200.bed.split13877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13878 0 1 2 100 hg38.150200.bed.split13878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13879 0 1 2 100 hg38.150200.bed.split13879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1388 0 1 2 100 hg38.150200.bed.split1388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13880 0 1 2 100 hg38.150200.bed.split13880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13881 0 1 2 100 hg38.150200.bed.split13881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13882 0 1 2 100 hg38.150200.bed.split13882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13883 0 1 2 100 hg38.150200.bed.split13883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13884 0 1 2 100 hg38.150200.bed.split13884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13885 0 1 2 100 hg38.150200.bed.split13885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13886 0 1 2 100 hg38.150200.bed.split13886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13887 0 1 2 100 hg38.150200.bed.split13887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13888 0 1 2 100 hg38.150200.bed.split13888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13889 0 1 2 100 hg38.150200.bed.split13889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1389 0 1 2 100 hg38.150200.bed.split1389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13890 0 1 2 100 hg38.150200.bed.split13890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13891 0 1 2 100 hg38.150200.bed.split13891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13892 0 1 2 100 hg38.150200.bed.split13892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13893 0 1 2 100 hg38.150200.bed.split13893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13894 0 1 2 100 hg38.150200.bed.split13894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13895 0 1 2 100 hg38.150200.bed.split13895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13896 0 1 2 100 hg38.150200.bed.split13896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13897 0 1 2 100 hg38.150200.bed.split13897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13898 0 1 2 100 hg38.150200.bed.split13898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13899 0 1 2 100 hg38.150200.bed.split13899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split139 0 1 2 100 hg38.150200.bed.split139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1390 0 1 2 100 hg38.150200.bed.split1390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13900 0 1 2 100 hg38.150200.bed.split13900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13901 0 1 2 100 hg38.150200.bed.split13901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13902 0 1 2 100 hg38.150200.bed.split13902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13903 0 1 2 100 hg38.150200.bed.split13903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13904 0 1 2 100 hg38.150200.bed.split13904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13905 0 1 2 100 hg38.150200.bed.split13905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13906 0 1 2 100 hg38.150200.bed.split13906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13907 0 1 2 100 hg38.150200.bed.split13907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13908 0 1 2 100 hg38.150200.bed.split13908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13909 0 1 2 100 hg38.150200.bed.split13909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1391 0 1 2 100 hg38.150200.bed.split1391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13910 0 1 2 100 hg38.150200.bed.split13910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13911 0 1 2 100 hg38.150200.bed.split13911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13912 0 1 2 100 hg38.150200.bed.split13912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13913 0 1 2 100 hg38.150200.bed.split13913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13914 0 1 2 100 hg38.150200.bed.split13914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13915 0 1 2 100 hg38.150200.bed.split13915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13916 0 1 2 100 hg38.150200.bed.split13916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13917 0 1 2 100 hg38.150200.bed.split13917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13918 0 1 2 100 hg38.150200.bed.split13918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13919 0 1 2 100 hg38.150200.bed.split13919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1392 0 1 2 100 hg38.150200.bed.split1392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13920 0 1 2 100 hg38.150200.bed.split13920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13921 0 1 2 100 hg38.150200.bed.split13921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13922 0 1 2 100 hg38.150200.bed.split13922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13923 0 1 2 100 hg38.150200.bed.split13923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13924 0 1 2 100 hg38.150200.bed.split13924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13925 0 1 2 100 hg38.150200.bed.split13925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13926 0 1 2 100 hg38.150200.bed.split13926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13927 0 1 2 100 hg38.150200.bed.split13927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13928 0 1 2 100 hg38.150200.bed.split13928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13929 0 1 2 100 hg38.150200.bed.split13929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1393 0 1 2 100 hg38.150200.bed.split1393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13930 0 1 2 100 hg38.150200.bed.split13930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13931 0 1 2 100 hg38.150200.bed.split13931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13932 0 1 2 100 hg38.150200.bed.split13932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13933 0 1 2 100 hg38.150200.bed.split13933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13934 0 1 2 100 hg38.150200.bed.split13934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13935 0 1 2 100 hg38.150200.bed.split13935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13936 0 1 2 100 hg38.150200.bed.split13936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13937 0 1 2 100 hg38.150200.bed.split13937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13938 0 1 2 100 hg38.150200.bed.split13938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13939 0 1 2 100 hg38.150200.bed.split13939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1394 0 1 2 100 hg38.150200.bed.split1394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13940 0 1 2 100 hg38.150200.bed.split13940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13941 0 1 2 100 hg38.150200.bed.split13941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13942 0 1 2 100 hg38.150200.bed.split13942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13943 0 1 2 100 hg38.150200.bed.split13943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13944 0 1 2 100 hg38.150200.bed.split13944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13945 0 1 2 100 hg38.150200.bed.split13945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13946 0 1 2 100 hg38.150200.bed.split13946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13947 0 1 2 100 hg38.150200.bed.split13947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13948 0 1 2 100 hg38.150200.bed.split13948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13949 0 1 2 100 hg38.150200.bed.split13949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1395 0 1 2 100 hg38.150200.bed.split1395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13950 0 1 2 100 hg38.150200.bed.split13950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13951 0 1 2 100 hg38.150200.bed.split13951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13952 0 1 2 100 hg38.150200.bed.split13952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13953 0 1 2 100 hg38.150200.bed.split13953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13954 0 1 2 100 hg38.150200.bed.split13954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13955 0 1 2 100 hg38.150200.bed.split13955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13956 0 1 2 100 hg38.150200.bed.split13956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13957 0 1 2 100 hg38.150200.bed.split13957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13958 0 1 2 100 hg38.150200.bed.split13958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13959 0 1 2 100 hg38.150200.bed.split13959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1396 0 1 2 100 hg38.150200.bed.split1396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13960 0 1 2 100 hg38.150200.bed.split13960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13961 0 1 2 100 hg38.150200.bed.split13961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13962 0 1 2 100 hg38.150200.bed.split13962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13963 0 1 2 100 hg38.150200.bed.split13963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13964 0 1 2 100 hg38.150200.bed.split13964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13965 0 1 2 100 hg38.150200.bed.split13965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13966 0 1 2 100 hg38.150200.bed.split13966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13967 0 1 2 100 hg38.150200.bed.split13967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13968 0 1 2 100 hg38.150200.bed.split13968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13969 0 1 2 100 hg38.150200.bed.split13969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1397 0 1 2 100 hg38.150200.bed.split1397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13970 0 1 2 100 hg38.150200.bed.split13970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13971 0 1 2 100 hg38.150200.bed.split13971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13972 0 1 2 100 hg38.150200.bed.split13972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13973 0 1 2 100 hg38.150200.bed.split13973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13974 0 1 2 100 hg38.150200.bed.split13974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13975 0 1 2 100 hg38.150200.bed.split13975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13976 0 1 2 100 hg38.150200.bed.split13976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13977 0 1 2 100 hg38.150200.bed.split13977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13978 0 1 2 100 hg38.150200.bed.split13978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13979 0 1 2 100 hg38.150200.bed.split13979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1398 0 1 2 100 hg38.150200.bed.split1398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13980 0 1 2 100 hg38.150200.bed.split13980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13981 0 1 2 100 hg38.150200.bed.split13981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13982 0 1 2 100 hg38.150200.bed.split13982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13983 0 1 2 100 hg38.150200.bed.split13983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13984 0 1 2 100 hg38.150200.bed.split13984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13985 0 1 2 100 hg38.150200.bed.split13985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13986 0 1 2 100 hg38.150200.bed.split13986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13987 0 1 2 100 hg38.150200.bed.split13987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13988 0 1 2 100 hg38.150200.bed.split13988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13989 0 1 2 100 hg38.150200.bed.split13989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1399 0 1 2 100 hg38.150200.bed.split1399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13990 0 1 2 100 hg38.150200.bed.split13990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13991 0 1 2 100 hg38.150200.bed.split13991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13992 0 1 2 100 hg38.150200.bed.split13992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13993 0 1 2 100 hg38.150200.bed.split13993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13994 0 1 2 100 hg38.150200.bed.split13994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13995 0 1 2 100 hg38.150200.bed.split13995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13996 0 1 2 100 hg38.150200.bed.split13996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13997 0 1 2 100 hg38.150200.bed.split13997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13998 0 1 2 100 hg38.150200.bed.split13998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split13999 0 1 2 100 hg38.150200.bed.split13999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14 0 1 2 100 hg38.150200.bed.split14.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split140 0 1 2 100 hg38.150200.bed.split140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1400 0 1 2 100 hg38.150200.bed.split1400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14000 0 1 2 100 hg38.150200.bed.split14000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14001 0 1 2 100 hg38.150200.bed.split14001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14002 0 1 2 100 hg38.150200.bed.split14002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14003 0 1 2 100 hg38.150200.bed.split14003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14004 0 1 2 100 hg38.150200.bed.split14004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14005 0 1 2 100 hg38.150200.bed.split14005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14006 0 1 2 100 hg38.150200.bed.split14006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14007 0 1 2 100 hg38.150200.bed.split14007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14008 0 1 2 100 hg38.150200.bed.split14008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14009 0 1 2 100 hg38.150200.bed.split14009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1401 0 1 2 100 hg38.150200.bed.split1401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14010 0 1 2 100 hg38.150200.bed.split14010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14011 0 1 2 100 hg38.150200.bed.split14011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14012 0 1 2 100 hg38.150200.bed.split14012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14013 0 1 2 100 hg38.150200.bed.split14013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14014 0 1 2 100 hg38.150200.bed.split14014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14015 0 1 2 100 hg38.150200.bed.split14015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14016 0 1 2 100 hg38.150200.bed.split14016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14017 0 1 2 100 hg38.150200.bed.split14017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14018 0 1 2 100 hg38.150200.bed.split14018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14019 0 1 2 100 hg38.150200.bed.split14019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1402 0 1 2 100 hg38.150200.bed.split1402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14020 0 1 2 100 hg38.150200.bed.split14020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14021 0 1 2 100 hg38.150200.bed.split14021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14022 0 1 2 100 hg38.150200.bed.split14022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14023 0 1 2 100 hg38.150200.bed.split14023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14024 0 1 2 100 hg38.150200.bed.split14024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14025 0 1 2 100 hg38.150200.bed.split14025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14026 0 1 2 100 hg38.150200.bed.split14026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14027 0 1 2 100 hg38.150200.bed.split14027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14028 0 1 2 100 hg38.150200.bed.split14028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14029 0 1 2 100 hg38.150200.bed.split14029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1403 0 1 2 100 hg38.150200.bed.split1403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14030 0 1 2 100 hg38.150200.bed.split14030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14031 0 1 2 100 hg38.150200.bed.split14031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14032 0 1 2 100 hg38.150200.bed.split14032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14033 0 1 2 100 hg38.150200.bed.split14033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14034 0 1 2 100 hg38.150200.bed.split14034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14035 0 1 2 100 hg38.150200.bed.split14035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14036 0 1 2 100 hg38.150200.bed.split14036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14037 0 1 2 100 hg38.150200.bed.split14037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14038 0 1 2 100 hg38.150200.bed.split14038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14039 0 1 2 100 hg38.150200.bed.split14039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1404 0 1 2 100 hg38.150200.bed.split1404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14040 0 1 2 100 hg38.150200.bed.split14040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14041 0 1 2 100 hg38.150200.bed.split14041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14042 0 1 2 100 hg38.150200.bed.split14042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14043 0 1 2 100 hg38.150200.bed.split14043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14044 0 1 2 100 hg38.150200.bed.split14044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14045 0 1 2 100 hg38.150200.bed.split14045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14046 0 1 2 100 hg38.150200.bed.split14046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14047 0 1 2 100 hg38.150200.bed.split14047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14048 0 1 2 100 hg38.150200.bed.split14048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14049 0 1 2 100 hg38.150200.bed.split14049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1405 0 1 2 100 hg38.150200.bed.split1405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14050 0 1 2 100 hg38.150200.bed.split14050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14051 0 1 2 100 hg38.150200.bed.split14051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14052 0 1 2 100 hg38.150200.bed.split14052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14053 0 1 2 100 hg38.150200.bed.split14053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14054 0 1 2 100 hg38.150200.bed.split14054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14055 0 1 2 100 hg38.150200.bed.split14055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14056 0 1 2 100 hg38.150200.bed.split14056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14057 0 1 2 100 hg38.150200.bed.split14057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14058 0 1 2 100 hg38.150200.bed.split14058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14059 0 1 2 100 hg38.150200.bed.split14059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1406 0 1 2 100 hg38.150200.bed.split1406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14060 0 1 2 100 hg38.150200.bed.split14060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14061 0 1 2 100 hg38.150200.bed.split14061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14062 0 1 2 100 hg38.150200.bed.split14062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14063 0 1 2 100 hg38.150200.bed.split14063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14064 0 1 2 100 hg38.150200.bed.split14064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14065 0 1 2 100 hg38.150200.bed.split14065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14066 0 1 2 100 hg38.150200.bed.split14066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14067 0 1 2 100 hg38.150200.bed.split14067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14068 0 1 2 100 hg38.150200.bed.split14068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14069 0 1 2 100 hg38.150200.bed.split14069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1407 0 1 2 100 hg38.150200.bed.split1407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14070 0 1 2 100 hg38.150200.bed.split14070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14071 0 1 2 100 hg38.150200.bed.split14071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14072 0 1 2 100 hg38.150200.bed.split14072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14073 0 1 2 100 hg38.150200.bed.split14073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14074 0 1 2 100 hg38.150200.bed.split14074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14075 0 1 2 100 hg38.150200.bed.split14075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14076 0 1 2 100 hg38.150200.bed.split14076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14077 0 1 2 100 hg38.150200.bed.split14077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14078 0 1 2 100 hg38.150200.bed.split14078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14079 0 1 2 100 hg38.150200.bed.split14079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1408 0 1 2 100 hg38.150200.bed.split1408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14080 0 1 2 100 hg38.150200.bed.split14080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14081 0 1 2 100 hg38.150200.bed.split14081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14082 0 1 2 100 hg38.150200.bed.split14082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14083 0 1 2 100 hg38.150200.bed.split14083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14084 0 1 2 100 hg38.150200.bed.split14084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14085 0 1 2 100 hg38.150200.bed.split14085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14086 0 1 2 100 hg38.150200.bed.split14086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14087 0 1 2 100 hg38.150200.bed.split14087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14088 0 1 2 100 hg38.150200.bed.split14088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14089 0 1 2 100 hg38.150200.bed.split14089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1409 0 1 2 100 hg38.150200.bed.split1409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14090 0 1 2 100 hg38.150200.bed.split14090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14091 0 1 2 100 hg38.150200.bed.split14091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14092 0 1 2 100 hg38.150200.bed.split14092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14093 0 1 2 100 hg38.150200.bed.split14093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14094 0 1 2 100 hg38.150200.bed.split14094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14095 0 1 2 100 hg38.150200.bed.split14095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14096 0 1 2 100 hg38.150200.bed.split14096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14097 0 1 2 100 hg38.150200.bed.split14097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14098 0 1 2 100 hg38.150200.bed.split14098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14099 0 1 2 100 hg38.150200.bed.split14099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split141 0 1 2 100 hg38.150200.bed.split141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1410 0 1 2 100 hg38.150200.bed.split1410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14100 0 1 2 100 hg38.150200.bed.split14100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14101 0 1 2 100 hg38.150200.bed.split14101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14102 0 1 2 100 hg38.150200.bed.split14102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14103 0 1 2 100 hg38.150200.bed.split14103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14104 0 1 2 100 hg38.150200.bed.split14104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14105 0 1 2 100 hg38.150200.bed.split14105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14106 0 1 2 100 hg38.150200.bed.split14106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14107 0 1 2 100 hg38.150200.bed.split14107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14108 0 1 2 100 hg38.150200.bed.split14108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14109 0 1 2 100 hg38.150200.bed.split14109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1411 0 1 2 100 hg38.150200.bed.split1411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14110 0 1 2 100 hg38.150200.bed.split14110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14111 0 1 2 100 hg38.150200.bed.split14111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14112 0 1 2 100 hg38.150200.bed.split14112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14113 0 1 2 100 hg38.150200.bed.split14113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14114 0 1 2 100 hg38.150200.bed.split14114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14115 0 1 2 100 hg38.150200.bed.split14115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14116 0 1 2 100 hg38.150200.bed.split14116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14117 0 1 2 100 hg38.150200.bed.split14117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14118 0 1 2 100 hg38.150200.bed.split14118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14119 0 1 2 100 hg38.150200.bed.split14119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1412 0 1 2 100 hg38.150200.bed.split1412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14120 0 1 2 100 hg38.150200.bed.split14120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14121 0 1 2 100 hg38.150200.bed.split14121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14122 0 1 2 100 hg38.150200.bed.split14122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14123 0 1 2 100 hg38.150200.bed.split14123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14124 0 1 2 100 hg38.150200.bed.split14124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14125 0 1 2 100 hg38.150200.bed.split14125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14126 0 1 2 100 hg38.150200.bed.split14126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14127 0 1 2 100 hg38.150200.bed.split14127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14128 0 1 2 100 hg38.150200.bed.split14128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14129 0 1 2 100 hg38.150200.bed.split14129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1413 0 1 2 100 hg38.150200.bed.split1413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14130 0 1 2 100 hg38.150200.bed.split14130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14131 0 1 2 100 hg38.150200.bed.split14131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14132 0 1 2 100 hg38.150200.bed.split14132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14133 0 1 2 100 hg38.150200.bed.split14133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14134 0 1 2 100 hg38.150200.bed.split14134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14135 0 1 2 100 hg38.150200.bed.split14135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14136 0 1 2 100 hg38.150200.bed.split14136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14137 0 1 2 100 hg38.150200.bed.split14137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14138 0 1 2 100 hg38.150200.bed.split14138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14139 0 1 2 100 hg38.150200.bed.split14139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1414 0 1 2 100 hg38.150200.bed.split1414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14140 0 1 2 100 hg38.150200.bed.split14140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14141 0 1 2 100 hg38.150200.bed.split14141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14142 0 1 2 100 hg38.150200.bed.split14142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14143 0 1 2 100 hg38.150200.bed.split14143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14144 0 1 2 100 hg38.150200.bed.split14144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14145 0 1 2 100 hg38.150200.bed.split14145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14146 0 1 2 100 hg38.150200.bed.split14146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14147 0 1 2 100 hg38.150200.bed.split14147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14148 0 1 2 100 hg38.150200.bed.split14148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14149 0 1 2 100 hg38.150200.bed.split14149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1415 0 1 2 100 hg38.150200.bed.split1415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14150 0 1 2 100 hg38.150200.bed.split14150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14151 0 1 2 100 hg38.150200.bed.split14151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14152 0 1 2 100 hg38.150200.bed.split14152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14153 0 1 2 100 hg38.150200.bed.split14153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14154 0 1 2 100 hg38.150200.bed.split14154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14155 0 1 2 100 hg38.150200.bed.split14155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14156 0 1 2 100 hg38.150200.bed.split14156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14157 0 1 2 100 hg38.150200.bed.split14157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14158 0 1 2 100 hg38.150200.bed.split14158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14159 0 1 2 100 hg38.150200.bed.split14159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1416 0 1 2 100 hg38.150200.bed.split1416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14160 0 1 2 100 hg38.150200.bed.split14160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14161 0 1 2 100 hg38.150200.bed.split14161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14162 0 1 2 100 hg38.150200.bed.split14162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14163 0 1 2 100 hg38.150200.bed.split14163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14164 0 1 2 100 hg38.150200.bed.split14164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14165 0 1 2 100 hg38.150200.bed.split14165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14166 0 1 2 100 hg38.150200.bed.split14166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14167 0 1 2 100 hg38.150200.bed.split14167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14168 0 1 2 100 hg38.150200.bed.split14168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14169 0 1 2 100 hg38.150200.bed.split14169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1417 0 1 2 100 hg38.150200.bed.split1417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14170 0 1 2 100 hg38.150200.bed.split14170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14171 0 1 2 100 hg38.150200.bed.split14171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14172 0 1 2 100 hg38.150200.bed.split14172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14173 0 1 2 100 hg38.150200.bed.split14173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14174 0 1 2 100 hg38.150200.bed.split14174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14175 0 1 2 100 hg38.150200.bed.split14175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14176 0 1 2 100 hg38.150200.bed.split14176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14177 0 1 2 100 hg38.150200.bed.split14177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14178 0 1 2 100 hg38.150200.bed.split14178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14179 0 1 2 100 hg38.150200.bed.split14179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1418 0 1 2 100 hg38.150200.bed.split1418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14180 0 1 2 100 hg38.150200.bed.split14180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14181 0 1 2 100 hg38.150200.bed.split14181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14182 0 1 2 100 hg38.150200.bed.split14182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14183 0 1 2 100 hg38.150200.bed.split14183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14184 0 1 2 100 hg38.150200.bed.split14184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14185 0 1 2 100 hg38.150200.bed.split14185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14186 0 1 2 100 hg38.150200.bed.split14186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14187 0 1 2 100 hg38.150200.bed.split14187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14188 0 1 2 100 hg38.150200.bed.split14188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14189 0 1 2 100 hg38.150200.bed.split14189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1419 0 1 2 100 hg38.150200.bed.split1419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14190 0 1 2 100 hg38.150200.bed.split14190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14191 0 1 2 100 hg38.150200.bed.split14191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14192 0 1 2 100 hg38.150200.bed.split14192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14193 0 1 2 100 hg38.150200.bed.split14193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14194 0 1 2 100 hg38.150200.bed.split14194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14195 0 1 2 100 hg38.150200.bed.split14195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14196 0 1 2 100 hg38.150200.bed.split14196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14197 0 1 2 100 hg38.150200.bed.split14197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14198 0 1 2 100 hg38.150200.bed.split14198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14199 0 1 2 100 hg38.150200.bed.split14199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split142 0 1 2 100 hg38.150200.bed.split142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1420 0 1 2 100 hg38.150200.bed.split1420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14200 0 1 2 100 hg38.150200.bed.split14200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14201 0 1 2 100 hg38.150200.bed.split14201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14202 0 1 2 100 hg38.150200.bed.split14202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14203 0 1 2 100 hg38.150200.bed.split14203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14204 0 1 2 100 hg38.150200.bed.split14204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14205 0 1 2 100 hg38.150200.bed.split14205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14206 0 1 2 100 hg38.150200.bed.split14206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14207 0 1 2 100 hg38.150200.bed.split14207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14208 0 1 2 100 hg38.150200.bed.split14208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14209 0 1 2 100 hg38.150200.bed.split14209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1421 0 1 2 100 hg38.150200.bed.split1421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14210 0 1 2 100 hg38.150200.bed.split14210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14211 0 1 2 100 hg38.150200.bed.split14211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14212 0 1 2 100 hg38.150200.bed.split14212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14213 0 1 2 100 hg38.150200.bed.split14213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14214 0 1 2 100 hg38.150200.bed.split14214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14215 0 1 2 100 hg38.150200.bed.split14215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14216 0 1 2 100 hg38.150200.bed.split14216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14217 0 1 2 100 hg38.150200.bed.split14217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14218 0 1 2 100 hg38.150200.bed.split14218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14219 0 1 2 100 hg38.150200.bed.split14219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1422 0 1 2 100 hg38.150200.bed.split1422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14220 0 1 2 100 hg38.150200.bed.split14220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14221 0 1 2 100 hg38.150200.bed.split14221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14222 0 1 2 100 hg38.150200.bed.split14222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14223 0 1 2 100 hg38.150200.bed.split14223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14224 0 1 2 100 hg38.150200.bed.split14224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14225 0 1 2 100 hg38.150200.bed.split14225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14226 0 1 2 100 hg38.150200.bed.split14226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14227 0 1 2 100 hg38.150200.bed.split14227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14228 0 1 2 100 hg38.150200.bed.split14228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14229 0 1 2 100 hg38.150200.bed.split14229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1423 0 1 2 100 hg38.150200.bed.split1423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14230 0 1 2 100 hg38.150200.bed.split14230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14231 0 1 2 100 hg38.150200.bed.split14231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14232 0 1 2 100 hg38.150200.bed.split14232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14233 0 1 2 100 hg38.150200.bed.split14233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14234 0 1 2 100 hg38.150200.bed.split14234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14235 0 1 2 100 hg38.150200.bed.split14235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14236 0 1 2 100 hg38.150200.bed.split14236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14237 0 1 2 100 hg38.150200.bed.split14237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14238 0 1 2 100 hg38.150200.bed.split14238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14239 0 1 2 100 hg38.150200.bed.split14239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1424 0 1 2 100 hg38.150200.bed.split1424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14240 0 1 2 100 hg38.150200.bed.split14240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14241 0 1 2 100 hg38.150200.bed.split14241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14242 0 1 2 100 hg38.150200.bed.split14242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14243 0 1 2 100 hg38.150200.bed.split14243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14244 0 1 2 100 hg38.150200.bed.split14244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14245 0 1 2 100 hg38.150200.bed.split14245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14246 0 1 2 100 hg38.150200.bed.split14246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14247 0 1 2 100 hg38.150200.bed.split14247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14248 0 1 2 100 hg38.150200.bed.split14248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14249 0 1 2 100 hg38.150200.bed.split14249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1425 0 1 2 100 hg38.150200.bed.split1425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14250 0 1 2 100 hg38.150200.bed.split14250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14251 0 1 2 100 hg38.150200.bed.split14251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14252 0 1 2 100 hg38.150200.bed.split14252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14253 0 1 2 100 hg38.150200.bed.split14253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14254 0 1 2 100 hg38.150200.bed.split14254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14255 0 1 2 100 hg38.150200.bed.split14255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14256 0 1 2 100 hg38.150200.bed.split14256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14257 0 1 2 100 hg38.150200.bed.split14257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14258 0 1 2 100 hg38.150200.bed.split14258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14259 0 1 2 100 hg38.150200.bed.split14259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1426 0 1 2 100 hg38.150200.bed.split1426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14260 0 1 2 100 hg38.150200.bed.split14260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14261 0 1 2 100 hg38.150200.bed.split14261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14262 0 1 2 100 hg38.150200.bed.split14262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14263 0 1 2 100 hg38.150200.bed.split14263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14264 0 1 2 100 hg38.150200.bed.split14264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14265 0 1 2 100 hg38.150200.bed.split14265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14266 0 1 2 100 hg38.150200.bed.split14266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14267 0 1 2 100 hg38.150200.bed.split14267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14268 0 1 2 100 hg38.150200.bed.split14268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14269 0 1 2 100 hg38.150200.bed.split14269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1427 0 1 2 100 hg38.150200.bed.split1427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14270 0 1 2 100 hg38.150200.bed.split14270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14271 0 1 2 100 hg38.150200.bed.split14271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14272 0 1 2 100 hg38.150200.bed.split14272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14273 0 1 2 100 hg38.150200.bed.split14273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14274 0 1 2 100 hg38.150200.bed.split14274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14275 0 1 2 100 hg38.150200.bed.split14275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14276 0 1 2 100 hg38.150200.bed.split14276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14277 0 1 2 100 hg38.150200.bed.split14277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14278 0 1 2 100 hg38.150200.bed.split14278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14279 0 1 2 100 hg38.150200.bed.split14279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1428 0 1 2 100 hg38.150200.bed.split1428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14280 0 1 2 100 hg38.150200.bed.split14280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14281 0 1 2 100 hg38.150200.bed.split14281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14282 0 1 2 100 hg38.150200.bed.split14282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14283 0 1 2 100 hg38.150200.bed.split14283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14284 0 1 2 100 hg38.150200.bed.split14284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14285 0 1 2 100 hg38.150200.bed.split14285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14286 0 1 2 100 hg38.150200.bed.split14286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14287 0 1 2 100 hg38.150200.bed.split14287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14288 0 1 2 100 hg38.150200.bed.split14288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14289 0 1 2 100 hg38.150200.bed.split14289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1429 0 1 2 100 hg38.150200.bed.split1429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14290 0 1 2 100 hg38.150200.bed.split14290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14291 0 1 2 100 hg38.150200.bed.split14291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14292 0 1 2 100 hg38.150200.bed.split14292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14293 0 1 2 100 hg38.150200.bed.split14293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14294 0 1 2 100 hg38.150200.bed.split14294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14295 0 1 2 100 hg38.150200.bed.split14295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14296 0 1 2 100 hg38.150200.bed.split14296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14297 0 1 2 100 hg38.150200.bed.split14297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14298 0 1 2 100 hg38.150200.bed.split14298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14299 0 1 2 100 hg38.150200.bed.split14299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split143 0 1 2 100 hg38.150200.bed.split143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1430 0 1 2 100 hg38.150200.bed.split1430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14300 0 1 2 100 hg38.150200.bed.split14300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14301 0 1 2 100 hg38.150200.bed.split14301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14302 0 1 2 100 hg38.150200.bed.split14302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14303 0 1 2 100 hg38.150200.bed.split14303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14304 0 1 2 100 hg38.150200.bed.split14304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14305 0 1 2 100 hg38.150200.bed.split14305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14306 0 1 2 100 hg38.150200.bed.split14306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14307 0 1 2 100 hg38.150200.bed.split14307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14308 0 1 2 100 hg38.150200.bed.split14308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14309 0 1 2 100 hg38.150200.bed.split14309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1431 0 1 2 100 hg38.150200.bed.split1431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14310 0 1 2 100 hg38.150200.bed.split14310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14311 0 1 2 100 hg38.150200.bed.split14311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14312 0 1 2 100 hg38.150200.bed.split14312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14313 0 1 2 100 hg38.150200.bed.split14313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14314 0 1 2 100 hg38.150200.bed.split14314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14315 0 1 2 100 hg38.150200.bed.split14315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14316 0 1 2 100 hg38.150200.bed.split14316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14317 0 1 2 100 hg38.150200.bed.split14317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14318 0 1 2 100 hg38.150200.bed.split14318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14319 0 1 2 100 hg38.150200.bed.split14319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1432 0 1 2 100 hg38.150200.bed.split1432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14320 0 1 2 100 hg38.150200.bed.split14320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14321 0 1 2 100 hg38.150200.bed.split14321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14322 0 1 2 100 hg38.150200.bed.split14322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14323 0 1 2 100 hg38.150200.bed.split14323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14324 0 1 2 100 hg38.150200.bed.split14324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14325 0 1 2 100 hg38.150200.bed.split14325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14326 0 1 2 100 hg38.150200.bed.split14326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14327 0 1 2 100 hg38.150200.bed.split14327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14328 0 1 2 100 hg38.150200.bed.split14328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14329 0 1 2 100 hg38.150200.bed.split14329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1433 0 1 2 100 hg38.150200.bed.split1433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14330 0 1 2 100 hg38.150200.bed.split14330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14331 0 1 2 100 hg38.150200.bed.split14331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14332 0 1 2 100 hg38.150200.bed.split14332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14333 0 1 2 100 hg38.150200.bed.split14333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14334 0 1 2 100 hg38.150200.bed.split14334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14335 0 1 2 100 hg38.150200.bed.split14335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14336 0 1 2 100 hg38.150200.bed.split14336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14337 0 1 2 100 hg38.150200.bed.split14337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14338 0 1 2 100 hg38.150200.bed.split14338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14339 0 1 2 100 hg38.150200.bed.split14339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1434 0 1 2 100 hg38.150200.bed.split1434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14340 0 1 2 100 hg38.150200.bed.split14340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14341 0 1 2 100 hg38.150200.bed.split14341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14342 0 1 2 100 hg38.150200.bed.split14342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14343 0 1 2 100 hg38.150200.bed.split14343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14344 0 1 2 100 hg38.150200.bed.split14344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14345 0 1 2 100 hg38.150200.bed.split14345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14346 0 1 2 100 hg38.150200.bed.split14346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14347 0 1 2 100 hg38.150200.bed.split14347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14348 0 1 2 100 hg38.150200.bed.split14348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14349 0 1 2 100 hg38.150200.bed.split14349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1435 0 1 2 100 hg38.150200.bed.split1435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14350 0 1 2 100 hg38.150200.bed.split14350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14351 0 1 2 100 hg38.150200.bed.split14351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14352 0 1 2 100 hg38.150200.bed.split14352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14353 0 1 2 100 hg38.150200.bed.split14353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14354 0 1 2 100 hg38.150200.bed.split14354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14355 0 1 2 100 hg38.150200.bed.split14355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14356 0 1 2 100 hg38.150200.bed.split14356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14357 0 1 2 100 hg38.150200.bed.split14357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14358 0 1 2 100 hg38.150200.bed.split14358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14359 0 1 2 100 hg38.150200.bed.split14359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1436 0 1 2 100 hg38.150200.bed.split1436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14360 0 1 2 100 hg38.150200.bed.split14360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14361 0 1 2 100 hg38.150200.bed.split14361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14362 0 1 2 100 hg38.150200.bed.split14362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14363 0 1 2 100 hg38.150200.bed.split14363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14364 0 1 2 100 hg38.150200.bed.split14364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14365 0 1 2 100 hg38.150200.bed.split14365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14366 0 1 2 100 hg38.150200.bed.split14366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14367 0 1 2 100 hg38.150200.bed.split14367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14368 0 1 2 100 hg38.150200.bed.split14368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14369 0 1 2 100 hg38.150200.bed.split14369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1437 0 1 2 100 hg38.150200.bed.split1437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14370 0 1 2 100 hg38.150200.bed.split14370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14371 0 1 2 100 hg38.150200.bed.split14371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14372 0 1 2 100 hg38.150200.bed.split14372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14373 0 1 2 100 hg38.150200.bed.split14373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14374 0 1 2 100 hg38.150200.bed.split14374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14375 0 1 2 100 hg38.150200.bed.split14375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14376 0 1 2 100 hg38.150200.bed.split14376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14377 0 1 2 100 hg38.150200.bed.split14377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14378 0 1 2 100 hg38.150200.bed.split14378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14379 0 1 2 100 hg38.150200.bed.split14379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1438 0 1 2 100 hg38.150200.bed.split1438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14380 0 1 2 100 hg38.150200.bed.split14380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14381 0 1 2 100 hg38.150200.bed.split14381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14382 0 1 2 100 hg38.150200.bed.split14382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14383 0 1 2 100 hg38.150200.bed.split14383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14384 0 1 2 100 hg38.150200.bed.split14384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14385 0 1 2 100 hg38.150200.bed.split14385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14386 0 1 2 100 hg38.150200.bed.split14386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14387 0 1 2 100 hg38.150200.bed.split14387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14388 0 1 2 100 hg38.150200.bed.split14388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14389 0 1 2 100 hg38.150200.bed.split14389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1439 0 1 2 100 hg38.150200.bed.split1439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14390 0 1 2 100 hg38.150200.bed.split14390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14391 0 1 2 100 hg38.150200.bed.split14391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14392 0 1 2 100 hg38.150200.bed.split14392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14393 0 1 2 100 hg38.150200.bed.split14393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14394 0 1 2 100 hg38.150200.bed.split14394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14395 0 1 2 100 hg38.150200.bed.split14395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14396 0 1 2 100 hg38.150200.bed.split14396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14397 0 1 2 100 hg38.150200.bed.split14397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14398 0 1 2 100 hg38.150200.bed.split14398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14399 0 1 2 100 hg38.150200.bed.split14399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split144 0 1 2 100 hg38.150200.bed.split144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1440 0 1 2 100 hg38.150200.bed.split1440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14400 0 1 2 100 hg38.150200.bed.split14400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14401 0 1 2 100 hg38.150200.bed.split14401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14402 0 1 2 100 hg38.150200.bed.split14402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14403 0 1 2 100 hg38.150200.bed.split14403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14404 0 1 2 100 hg38.150200.bed.split14404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14405 0 1 2 100 hg38.150200.bed.split14405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14406 0 1 2 100 hg38.150200.bed.split14406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14407 0 1 2 100 hg38.150200.bed.split14407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14408 0 1 2 100 hg38.150200.bed.split14408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14409 0 1 2 100 hg38.150200.bed.split14409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1441 0 1 2 100 hg38.150200.bed.split1441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14410 0 1 2 100 hg38.150200.bed.split14410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14411 0 1 2 100 hg38.150200.bed.split14411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14412 0 1 2 100 hg38.150200.bed.split14412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14413 0 1 2 100 hg38.150200.bed.split14413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14414 0 1 2 100 hg38.150200.bed.split14414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14415 0 1 2 100 hg38.150200.bed.split14415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14416 0 1 2 100 hg38.150200.bed.split14416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14417 0 1 2 100 hg38.150200.bed.split14417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14418 0 1 2 100 hg38.150200.bed.split14418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14419 0 1 2 100 hg38.150200.bed.split14419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1442 0 1 2 100 hg38.150200.bed.split1442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14420 0 1 2 100 hg38.150200.bed.split14420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14421 0 1 2 100 hg38.150200.bed.split14421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14422 0 1 2 100 hg38.150200.bed.split14422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14423 0 1 2 100 hg38.150200.bed.split14423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14424 0 1 2 100 hg38.150200.bed.split14424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14425 0 1 2 100 hg38.150200.bed.split14425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14426 0 1 2 100 hg38.150200.bed.split14426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14427 0 1 2 100 hg38.150200.bed.split14427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14428 0 1 2 100 hg38.150200.bed.split14428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14429 0 1 2 100 hg38.150200.bed.split14429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1443 0 1 2 100 hg38.150200.bed.split1443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14430 0 1 2 100 hg38.150200.bed.split14430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14431 0 1 2 100 hg38.150200.bed.split14431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14432 0 1 2 100 hg38.150200.bed.split14432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14433 0 1 2 100 hg38.150200.bed.split14433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14434 0 1 2 100 hg38.150200.bed.split14434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14435 0 1 2 100 hg38.150200.bed.split14435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14436 0 1 2 100 hg38.150200.bed.split14436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14437 0 1 2 100 hg38.150200.bed.split14437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14438 0 1 2 100 hg38.150200.bed.split14438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14439 0 1 2 100 hg38.150200.bed.split14439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1444 0 1 2 100 hg38.150200.bed.split1444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14440 0 1 2 100 hg38.150200.bed.split14440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14441 0 1 2 100 hg38.150200.bed.split14441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14442 0 1 2 100 hg38.150200.bed.split14442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14443 0 1 2 100 hg38.150200.bed.split14443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14444 0 1 2 100 hg38.150200.bed.split14444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14445 0 1 2 100 hg38.150200.bed.split14445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14446 0 1 2 100 hg38.150200.bed.split14446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14447 0 1 2 100 hg38.150200.bed.split14447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14448 0 1 2 100 hg38.150200.bed.split14448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14449 0 1 2 100 hg38.150200.bed.split14449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1445 0 1 2 100 hg38.150200.bed.split1445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14450 0 1 2 100 hg38.150200.bed.split14450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14451 0 1 2 100 hg38.150200.bed.split14451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14452 0 1 2 100 hg38.150200.bed.split14452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14453 0 1 2 100 hg38.150200.bed.split14453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14454 0 1 2 100 hg38.150200.bed.split14454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14455 0 1 2 100 hg38.150200.bed.split14455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14456 0 1 2 100 hg38.150200.bed.split14456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14457 0 1 2 100 hg38.150200.bed.split14457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14458 0 1 2 100 hg38.150200.bed.split14458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14459 0 1 2 100 hg38.150200.bed.split14459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1446 0 1 2 100 hg38.150200.bed.split1446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14460 0 1 2 100 hg38.150200.bed.split14460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14461 0 1 2 100 hg38.150200.bed.split14461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14462 0 1 2 100 hg38.150200.bed.split14462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14463 0 1 2 100 hg38.150200.bed.split14463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14464 0 1 2 100 hg38.150200.bed.split14464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14465 0 1 2 100 hg38.150200.bed.split14465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14466 0 1 2 100 hg38.150200.bed.split14466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14467 0 1 2 100 hg38.150200.bed.split14467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14468 0 1 2 100 hg38.150200.bed.split14468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14469 0 1 2 100 hg38.150200.bed.split14469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1447 0 1 2 100 hg38.150200.bed.split1447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14470 0 1 2 100 hg38.150200.bed.split14470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14471 0 1 2 100 hg38.150200.bed.split14471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14472 0 1 2 100 hg38.150200.bed.split14472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14473 0 1 2 100 hg38.150200.bed.split14473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14474 0 1 2 100 hg38.150200.bed.split14474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14475 0 1 2 100 hg38.150200.bed.split14475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14476 0 1 2 100 hg38.150200.bed.split14476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14477 0 1 2 100 hg38.150200.bed.split14477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14478 0 1 2 100 hg38.150200.bed.split14478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14479 0 1 2 100 hg38.150200.bed.split14479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1448 0 1 2 100 hg38.150200.bed.split1448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14480 0 1 2 100 hg38.150200.bed.split14480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14481 0 1 2 100 hg38.150200.bed.split14481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14482 0 1 2 100 hg38.150200.bed.split14482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14483 0 1 2 100 hg38.150200.bed.split14483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14484 0 1 2 100 hg38.150200.bed.split14484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14485 0 1 2 100 hg38.150200.bed.split14485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14486 0 1 2 100 hg38.150200.bed.split14486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14487 0 1 2 100 hg38.150200.bed.split14487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14488 0 1 2 100 hg38.150200.bed.split14488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14489 0 1 2 100 hg38.150200.bed.split14489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1449 0 1 2 100 hg38.150200.bed.split1449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14490 0 1 2 100 hg38.150200.bed.split14490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14491 0 1 2 100 hg38.150200.bed.split14491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14492 0 1 2 100 hg38.150200.bed.split14492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14493 0 1 2 100 hg38.150200.bed.split14493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14494 0 1 2 100 hg38.150200.bed.split14494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14495 0 1 2 100 hg38.150200.bed.split14495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14496 0 1 2 100 hg38.150200.bed.split14496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14497 0 1 2 100 hg38.150200.bed.split14497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14498 0 1 2 100 hg38.150200.bed.split14498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14499 0 1 2 100 hg38.150200.bed.split14499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split145 0 1 2 100 hg38.150200.bed.split145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1450 0 1 2 100 hg38.150200.bed.split1450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14500 0 1 2 100 hg38.150200.bed.split14500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14501 0 1 2 100 hg38.150200.bed.split14501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14502 0 1 2 100 hg38.150200.bed.split14502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14503 0 1 2 100 hg38.150200.bed.split14503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14504 0 1 2 100 hg38.150200.bed.split14504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14505 0 1 2 100 hg38.150200.bed.split14505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14506 0 1 2 100 hg38.150200.bed.split14506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14507 0 1 2 100 hg38.150200.bed.split14507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14508 0 1 2 100 hg38.150200.bed.split14508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14509 0 1 2 100 hg38.150200.bed.split14509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1451 0 1 2 100 hg38.150200.bed.split1451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14510 0 1 2 100 hg38.150200.bed.split14510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14511 0 1 2 100 hg38.150200.bed.split14511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14512 0 1 2 100 hg38.150200.bed.split14512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14513 0 1 2 100 hg38.150200.bed.split14513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14514 0 1 2 100 hg38.150200.bed.split14514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14515 0 1 2 100 hg38.150200.bed.split14515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14516 0 1 2 100 hg38.150200.bed.split14516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14517 0 1 2 100 hg38.150200.bed.split14517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14518 0 1 2 100 hg38.150200.bed.split14518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14519 0 1 2 100 hg38.150200.bed.split14519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1452 0 1 2 100 hg38.150200.bed.split1452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14520 0 1 2 100 hg38.150200.bed.split14520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14521 0 1 2 100 hg38.150200.bed.split14521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14522 0 1 2 100 hg38.150200.bed.split14522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14523 0 1 2 100 hg38.150200.bed.split14523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14524 0 1 2 100 hg38.150200.bed.split14524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14525 0 1 2 100 hg38.150200.bed.split14525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14526 0 1 2 100 hg38.150200.bed.split14526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14527 0 1 2 100 hg38.150200.bed.split14527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14528 0 1 2 100 hg38.150200.bed.split14528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14529 0 1 2 100 hg38.150200.bed.split14529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1453 0 1 2 100 hg38.150200.bed.split1453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14530 0 1 2 100 hg38.150200.bed.split14530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14531 0 1 2 100 hg38.150200.bed.split14531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14532 0 1 2 100 hg38.150200.bed.split14532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14533 0 1 2 100 hg38.150200.bed.split14533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14534 0 1 2 100 hg38.150200.bed.split14534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14535 0 1 2 100 hg38.150200.bed.split14535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14536 0 1 2 100 hg38.150200.bed.split14536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14537 0 1 2 100 hg38.150200.bed.split14537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14538 0 1 2 100 hg38.150200.bed.split14538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14539 0 1 2 100 hg38.150200.bed.split14539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1454 0 1 2 100 hg38.150200.bed.split1454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14540 0 1 2 100 hg38.150200.bed.split14540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14541 0 1 2 100 hg38.150200.bed.split14541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14542 0 1 2 100 hg38.150200.bed.split14542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14543 0 1 2 100 hg38.150200.bed.split14543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14544 0 1 2 100 hg38.150200.bed.split14544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14545 0 1 2 100 hg38.150200.bed.split14545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14546 0 1 2 100 hg38.150200.bed.split14546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14547 0 1 2 100 hg38.150200.bed.split14547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14548 0 1 2 100 hg38.150200.bed.split14548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14549 0 1 2 100 hg38.150200.bed.split14549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1455 0 1 2 100 hg38.150200.bed.split1455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14550 0 1 2 100 hg38.150200.bed.split14550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14551 0 1 2 100 hg38.150200.bed.split14551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14552 0 1 2 100 hg38.150200.bed.split14552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14553 0 1 2 100 hg38.150200.bed.split14553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14554 0 1 2 100 hg38.150200.bed.split14554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14555 0 1 2 100 hg38.150200.bed.split14555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14556 0 1 2 100 hg38.150200.bed.split14556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14557 0 1 2 100 hg38.150200.bed.split14557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14558 0 1 2 100 hg38.150200.bed.split14558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14559 0 1 2 100 hg38.150200.bed.split14559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1456 0 1 2 100 hg38.150200.bed.split1456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14560 0 1 2 100 hg38.150200.bed.split14560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14561 0 1 2 100 hg38.150200.bed.split14561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14562 0 1 2 100 hg38.150200.bed.split14562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14563 0 1 2 100 hg38.150200.bed.split14563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14564 0 1 2 100 hg38.150200.bed.split14564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14565 0 1 2 100 hg38.150200.bed.split14565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14566 0 1 2 100 hg38.150200.bed.split14566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14567 0 1 2 100 hg38.150200.bed.split14567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14568 0 1 2 100 hg38.150200.bed.split14568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14569 0 1 2 100 hg38.150200.bed.split14569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1457 0 1 2 100 hg38.150200.bed.split1457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14570 0 1 2 100 hg38.150200.bed.split14570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14571 0 1 2 100 hg38.150200.bed.split14571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14572 0 1 2 100 hg38.150200.bed.split14572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14573 0 1 2 100 hg38.150200.bed.split14573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14574 0 1 2 100 hg38.150200.bed.split14574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14575 0 1 2 100 hg38.150200.bed.split14575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14576 0 1 2 100 hg38.150200.bed.split14576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14577 0 1 2 100 hg38.150200.bed.split14577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14578 0 1 2 100 hg38.150200.bed.split14578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14579 0 1 2 100 hg38.150200.bed.split14579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1458 0 1 2 100 hg38.150200.bed.split1458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14580 0 1 2 100 hg38.150200.bed.split14580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14581 0 1 2 100 hg38.150200.bed.split14581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14582 0 1 2 100 hg38.150200.bed.split14582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14583 0 1 2 100 hg38.150200.bed.split14583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14584 0 1 2 100 hg38.150200.bed.split14584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14585 0 1 2 100 hg38.150200.bed.split14585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14586 0 1 2 100 hg38.150200.bed.split14586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14587 0 1 2 100 hg38.150200.bed.split14587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14588 0 1 2 100 hg38.150200.bed.split14588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14589 0 1 2 100 hg38.150200.bed.split14589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1459 0 1 2 100 hg38.150200.bed.split1459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14590 0 1 2 100 hg38.150200.bed.split14590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14591 0 1 2 100 hg38.150200.bed.split14591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14592 0 1 2 100 hg38.150200.bed.split14592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14593 0 1 2 100 hg38.150200.bed.split14593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14594 0 1 2 100 hg38.150200.bed.split14594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14595 0 1 2 100 hg38.150200.bed.split14595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14596 0 1 2 100 hg38.150200.bed.split14596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14597 0 1 2 100 hg38.150200.bed.split14597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14598 0 1 2 100 hg38.150200.bed.split14598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14599 0 1 2 100 hg38.150200.bed.split14599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split146 0 1 2 100 hg38.150200.bed.split146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1460 0 1 2 100 hg38.150200.bed.split1460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14600 0 1 2 100 hg38.150200.bed.split14600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14601 0 1 2 100 hg38.150200.bed.split14601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14602 0 1 2 100 hg38.150200.bed.split14602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14603 0 1 2 100 hg38.150200.bed.split14603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14604 0 1 2 100 hg38.150200.bed.split14604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14605 0 1 2 100 hg38.150200.bed.split14605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14606 0 1 2 100 hg38.150200.bed.split14606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14607 0 1 2 100 hg38.150200.bed.split14607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14608 0 1 2 100 hg38.150200.bed.split14608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14609 0 1 2 100 hg38.150200.bed.split14609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1461 0 1 2 100 hg38.150200.bed.split1461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14610 0 1 2 100 hg38.150200.bed.split14610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14611 0 1 2 100 hg38.150200.bed.split14611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14612 0 1 2 100 hg38.150200.bed.split14612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14613 0 1 2 100 hg38.150200.bed.split14613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14614 0 1 2 100 hg38.150200.bed.split14614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14615 0 1 2 100 hg38.150200.bed.split14615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14616 0 1 2 100 hg38.150200.bed.split14616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14617 0 1 2 100 hg38.150200.bed.split14617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14618 0 1 2 100 hg38.150200.bed.split14618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14619 0 1 2 100 hg38.150200.bed.split14619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1462 0 1 2 100 hg38.150200.bed.split1462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14620 0 1 2 100 hg38.150200.bed.split14620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14621 0 1 2 100 hg38.150200.bed.split14621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14622 0 1 2 100 hg38.150200.bed.split14622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14623 0 1 2 100 hg38.150200.bed.split14623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14624 0 1 2 100 hg38.150200.bed.split14624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14625 0 1 2 100 hg38.150200.bed.split14625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14626 0 1 2 100 hg38.150200.bed.split14626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14627 0 1 2 100 hg38.150200.bed.split14627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14628 0 1 2 100 hg38.150200.bed.split14628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14629 0 1 2 100 hg38.150200.bed.split14629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1463 0 1 2 100 hg38.150200.bed.split1463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14630 0 1 2 100 hg38.150200.bed.split14630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14631 0 1 2 100 hg38.150200.bed.split14631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14632 0 1 2 100 hg38.150200.bed.split14632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14633 0 1 2 100 hg38.150200.bed.split14633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14634 0 1 2 100 hg38.150200.bed.split14634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14635 0 1 2 100 hg38.150200.bed.split14635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14636 0 1 2 100 hg38.150200.bed.split14636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14637 0 1 2 100 hg38.150200.bed.split14637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14638 0 1 2 100 hg38.150200.bed.split14638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14639 0 1 2 100 hg38.150200.bed.split14639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1464 0 1 2 100 hg38.150200.bed.split1464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14640 0 1 2 100 hg38.150200.bed.split14640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14641 0 1 2 100 hg38.150200.bed.split14641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14642 0 1 2 100 hg38.150200.bed.split14642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14643 0 1 2 100 hg38.150200.bed.split14643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14644 0 1 2 100 hg38.150200.bed.split14644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14645 0 1 2 100 hg38.150200.bed.split14645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14646 0 1 2 100 hg38.150200.bed.split14646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14647 0 1 2 100 hg38.150200.bed.split14647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14648 0 1 2 100 hg38.150200.bed.split14648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14649 0 1 2 100 hg38.150200.bed.split14649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1465 0 1 2 100 hg38.150200.bed.split1465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14650 0 1 2 100 hg38.150200.bed.split14650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14651 0 1 2 100 hg38.150200.bed.split14651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14652 0 1 2 100 hg38.150200.bed.split14652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14653 0 1 2 100 hg38.150200.bed.split14653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14654 0 1 2 100 hg38.150200.bed.split14654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14655 0 1 2 100 hg38.150200.bed.split14655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14656 0 1 2 100 hg38.150200.bed.split14656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14657 0 1 2 100 hg38.150200.bed.split14657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14658 0 1 2 100 hg38.150200.bed.split14658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14659 0 1 2 100 hg38.150200.bed.split14659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1466 0 1 2 100 hg38.150200.bed.split1466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14660 0 1 2 100 hg38.150200.bed.split14660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14661 0 1 2 100 hg38.150200.bed.split14661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14662 0 1 2 100 hg38.150200.bed.split14662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14663 0 1 2 100 hg38.150200.bed.split14663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14664 0 1 2 100 hg38.150200.bed.split14664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14665 0 1 2 100 hg38.150200.bed.split14665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14666 0 1 2 100 hg38.150200.bed.split14666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14667 0 1 2 100 hg38.150200.bed.split14667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14668 0 1 2 100 hg38.150200.bed.split14668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14669 0 1 2 100 hg38.150200.bed.split14669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1467 0 1 2 100 hg38.150200.bed.split1467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14670 0 1 2 100 hg38.150200.bed.split14670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14671 0 1 2 100 hg38.150200.bed.split14671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14672 0 1 2 100 hg38.150200.bed.split14672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14673 0 1 2 100 hg38.150200.bed.split14673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14674 0 1 2 100 hg38.150200.bed.split14674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14675 0 1 2 100 hg38.150200.bed.split14675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14676 0 1 2 100 hg38.150200.bed.split14676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14677 0 1 2 100 hg38.150200.bed.split14677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14678 0 1 2 100 hg38.150200.bed.split14678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14679 0 1 2 100 hg38.150200.bed.split14679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1468 0 1 2 100 hg38.150200.bed.split1468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14680 0 1 2 100 hg38.150200.bed.split14680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14681 0 1 2 100 hg38.150200.bed.split14681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14682 0 1 2 100 hg38.150200.bed.split14682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14683 0 1 2 100 hg38.150200.bed.split14683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14684 0 1 2 100 hg38.150200.bed.split14684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14685 0 1 2 100 hg38.150200.bed.split14685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14686 0 1 2 100 hg38.150200.bed.split14686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14687 0 1 2 100 hg38.150200.bed.split14687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14688 0 1 2 100 hg38.150200.bed.split14688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14689 0 1 2 100 hg38.150200.bed.split14689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1469 0 1 2 100 hg38.150200.bed.split1469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14690 0 1 2 100 hg38.150200.bed.split14690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14691 0 1 2 100 hg38.150200.bed.split14691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14692 0 1 2 100 hg38.150200.bed.split14692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14693 0 1 2 100 hg38.150200.bed.split14693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14694 0 1 2 100 hg38.150200.bed.split14694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14695 0 1 2 100 hg38.150200.bed.split14695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14696 0 1 2 100 hg38.150200.bed.split14696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14697 0 1 2 100 hg38.150200.bed.split14697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14698 0 1 2 100 hg38.150200.bed.split14698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14699 0 1 2 100 hg38.150200.bed.split14699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split147 0 1 2 100 hg38.150200.bed.split147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1470 0 1 2 100 hg38.150200.bed.split1470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14700 0 1 2 100 hg38.150200.bed.split14700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14701 0 1 2 100 hg38.150200.bed.split14701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14702 0 1 2 100 hg38.150200.bed.split14702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14703 0 1 2 100 hg38.150200.bed.split14703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14704 0 1 2 100 hg38.150200.bed.split14704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14705 0 1 2 100 hg38.150200.bed.split14705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14706 0 1 2 100 hg38.150200.bed.split14706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14707 0 1 2 100 hg38.150200.bed.split14707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14708 0 1 2 100 hg38.150200.bed.split14708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14709 0 1 2 100 hg38.150200.bed.split14709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1471 0 1 2 100 hg38.150200.bed.split1471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14710 0 1 2 100 hg38.150200.bed.split14710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14711 0 1 2 100 hg38.150200.bed.split14711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14712 0 1 2 100 hg38.150200.bed.split14712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14713 0 1 2 100 hg38.150200.bed.split14713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14714 0 1 2 100 hg38.150200.bed.split14714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14715 0 1 2 100 hg38.150200.bed.split14715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14716 0 1 2 100 hg38.150200.bed.split14716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14717 0 1 2 100 hg38.150200.bed.split14717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14718 0 1 2 100 hg38.150200.bed.split14718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14719 0 1 2 100 hg38.150200.bed.split14719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1472 0 1 2 100 hg38.150200.bed.split1472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14720 0 1 2 100 hg38.150200.bed.split14720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14721 0 1 2 100 hg38.150200.bed.split14721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14722 0 1 2 100 hg38.150200.bed.split14722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14723 0 1 2 100 hg38.150200.bed.split14723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14724 0 1 2 100 hg38.150200.bed.split14724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14725 0 1 2 100 hg38.150200.bed.split14725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14726 0 1 2 100 hg38.150200.bed.split14726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14727 0 1 2 100 hg38.150200.bed.split14727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14728 0 1 2 100 hg38.150200.bed.split14728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14729 0 1 2 100 hg38.150200.bed.split14729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1473 0 1 2 100 hg38.150200.bed.split1473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14730 0 1 2 100 hg38.150200.bed.split14730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14731 0 1 2 100 hg38.150200.bed.split14731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14732 0 1 2 100 hg38.150200.bed.split14732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14733 0 1 2 100 hg38.150200.bed.split14733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14734 0 1 2 100 hg38.150200.bed.split14734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14735 0 1 2 100 hg38.150200.bed.split14735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14736 0 1 2 100 hg38.150200.bed.split14736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14737 0 1 2 100 hg38.150200.bed.split14737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14738 0 1 2 100 hg38.150200.bed.split14738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14739 0 1 2 100 hg38.150200.bed.split14739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1474 0 1 2 100 hg38.150200.bed.split1474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14740 0 1 2 100 hg38.150200.bed.split14740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14741 0 1 2 100 hg38.150200.bed.split14741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14742 0 1 2 100 hg38.150200.bed.split14742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14743 0 1 2 100 hg38.150200.bed.split14743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14744 0 1 2 100 hg38.150200.bed.split14744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14745 0 1 2 100 hg38.150200.bed.split14745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14746 0 1 2 100 hg38.150200.bed.split14746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14747 0 1 2 100 hg38.150200.bed.split14747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14748 0 1 2 100 hg38.150200.bed.split14748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14749 0 1 2 100 hg38.150200.bed.split14749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1475 0 1 2 100 hg38.150200.bed.split1475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14750 0 1 2 100 hg38.150200.bed.split14750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14751 0 1 2 100 hg38.150200.bed.split14751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14752 0 1 2 100 hg38.150200.bed.split14752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14753 0 1 2 100 hg38.150200.bed.split14753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14754 0 1 2 100 hg38.150200.bed.split14754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14755 0 1 2 100 hg38.150200.bed.split14755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14756 0 1 2 100 hg38.150200.bed.split14756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14757 0 1 2 100 hg38.150200.bed.split14757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14758 0 1 2 100 hg38.150200.bed.split14758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14759 0 1 2 100 hg38.150200.bed.split14759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1476 0 1 2 100 hg38.150200.bed.split1476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14760 0 1 2 100 hg38.150200.bed.split14760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14761 0 1 2 100 hg38.150200.bed.split14761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14762 0 1 2 100 hg38.150200.bed.split14762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14763 0 1 2 100 hg38.150200.bed.split14763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14764 0 1 2 100 hg38.150200.bed.split14764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14765 0 1 2 100 hg38.150200.bed.split14765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14766 0 1 2 100 hg38.150200.bed.split14766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14767 0 1 2 100 hg38.150200.bed.split14767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14768 0 1 2 100 hg38.150200.bed.split14768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14769 0 1 2 100 hg38.150200.bed.split14769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1477 0 1 2 100 hg38.150200.bed.split1477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14770 0 1 2 100 hg38.150200.bed.split14770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14771 0 1 2 100 hg38.150200.bed.split14771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14772 0 1 2 100 hg38.150200.bed.split14772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14773 0 1 2 100 hg38.150200.bed.split14773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14774 0 1 2 100 hg38.150200.bed.split14774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14775 0 1 2 100 hg38.150200.bed.split14775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14776 0 1 2 100 hg38.150200.bed.split14776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14777 0 1 2 100 hg38.150200.bed.split14777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14778 0 1 2 100 hg38.150200.bed.split14778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14779 0 1 2 100 hg38.150200.bed.split14779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1478 0 1 2 100 hg38.150200.bed.split1478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14780 0 1 2 100 hg38.150200.bed.split14780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14781 0 1 2 100 hg38.150200.bed.split14781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14782 0 1 2 100 hg38.150200.bed.split14782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14783 0 1 2 100 hg38.150200.bed.split14783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14784 0 1 2 100 hg38.150200.bed.split14784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14785 0 1 2 100 hg38.150200.bed.split14785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14786 0 1 2 100 hg38.150200.bed.split14786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14787 0 1 2 100 hg38.150200.bed.split14787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14788 0 1 2 100 hg38.150200.bed.split14788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14789 0 1 2 100 hg38.150200.bed.split14789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1479 0 1 2 100 hg38.150200.bed.split1479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14790 0 1 2 100 hg38.150200.bed.split14790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14791 0 1 2 100 hg38.150200.bed.split14791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14792 0 1 2 100 hg38.150200.bed.split14792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14793 0 1 2 100 hg38.150200.bed.split14793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14794 0 1 2 100 hg38.150200.bed.split14794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14795 0 1 2 100 hg38.150200.bed.split14795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14796 0 1 2 100 hg38.150200.bed.split14796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14797 0 1 2 100 hg38.150200.bed.split14797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14798 0 1 2 100 hg38.150200.bed.split14798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14799 0 1 2 100 hg38.150200.bed.split14799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split148 0 1 2 100 hg38.150200.bed.split148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1480 0 1 2 100 hg38.150200.bed.split1480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14800 0 1 2 100 hg38.150200.bed.split14800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14801 0 1 2 100 hg38.150200.bed.split14801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14802 0 1 2 100 hg38.150200.bed.split14802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14803 0 1 2 100 hg38.150200.bed.split14803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14804 0 1 2 100 hg38.150200.bed.split14804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14805 0 1 2 100 hg38.150200.bed.split14805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14806 0 1 2 100 hg38.150200.bed.split14806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14807 0 1 2 100 hg38.150200.bed.split14807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14808 0 1 2 100 hg38.150200.bed.split14808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14809 0 1 2 100 hg38.150200.bed.split14809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1481 0 1 2 100 hg38.150200.bed.split1481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14810 0 1 2 100 hg38.150200.bed.split14810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14811 0 1 2 100 hg38.150200.bed.split14811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14812 0 1 2 100 hg38.150200.bed.split14812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14813 0 1 2 100 hg38.150200.bed.split14813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14814 0 1 2 100 hg38.150200.bed.split14814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14815 0 1 2 100 hg38.150200.bed.split14815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14816 0 1 2 100 hg38.150200.bed.split14816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14817 0 1 2 100 hg38.150200.bed.split14817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14818 0 1 2 100 hg38.150200.bed.split14818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14819 0 1 2 100 hg38.150200.bed.split14819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1482 0 1 2 100 hg38.150200.bed.split1482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14820 0 1 2 100 hg38.150200.bed.split14820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14821 0 1 2 100 hg38.150200.bed.split14821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14822 0 1 2 100 hg38.150200.bed.split14822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14823 0 1 2 100 hg38.150200.bed.split14823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14824 0 1 2 100 hg38.150200.bed.split14824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14825 0 1 2 100 hg38.150200.bed.split14825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14826 0 1 2 100 hg38.150200.bed.split14826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14827 0 1 2 100 hg38.150200.bed.split14827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14828 0 1 2 100 hg38.150200.bed.split14828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14829 0 1 2 100 hg38.150200.bed.split14829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1483 0 1 2 100 hg38.150200.bed.split1483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14830 0 1 2 100 hg38.150200.bed.split14830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14831 0 1 2 100 hg38.150200.bed.split14831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14832 0 1 2 100 hg38.150200.bed.split14832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14833 0 1 2 100 hg38.150200.bed.split14833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14834 0 1 2 100 hg38.150200.bed.split14834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14835 0 1 2 100 hg38.150200.bed.split14835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14836 0 1 2 100 hg38.150200.bed.split14836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14837 0 1 2 100 hg38.150200.bed.split14837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14838 0 1 2 100 hg38.150200.bed.split14838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14839 0 1 2 100 hg38.150200.bed.split14839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1484 0 1 2 100 hg38.150200.bed.split1484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14840 0 1 2 100 hg38.150200.bed.split14840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14841 0 1 2 100 hg38.150200.bed.split14841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14842 0 1 2 100 hg38.150200.bed.split14842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14843 0 1 2 100 hg38.150200.bed.split14843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14844 0 1 2 100 hg38.150200.bed.split14844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14845 0 1 2 100 hg38.150200.bed.split14845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14846 0 1 2 100 hg38.150200.bed.split14846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14847 0 1 2 100 hg38.150200.bed.split14847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14848 0 1 2 100 hg38.150200.bed.split14848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14849 0 1 2 100 hg38.150200.bed.split14849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1485 0 1 2 100 hg38.150200.bed.split1485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14850 0 1 2 100 hg38.150200.bed.split14850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14851 0 1 2 100 hg38.150200.bed.split14851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14852 0 1 2 100 hg38.150200.bed.split14852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14853 0 1 2 100 hg38.150200.bed.split14853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14854 0 1 2 100 hg38.150200.bed.split14854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14855 0 1 2 100 hg38.150200.bed.split14855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14856 0 1 2 100 hg38.150200.bed.split14856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14857 0 1 2 100 hg38.150200.bed.split14857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14858 0 1 2 100 hg38.150200.bed.split14858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14859 0 1 2 100 hg38.150200.bed.split14859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1486 0 1 2 100 hg38.150200.bed.split1486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14860 0 1 2 100 hg38.150200.bed.split14860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14861 0 1 2 100 hg38.150200.bed.split14861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14862 0 1 2 100 hg38.150200.bed.split14862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14863 0 1 2 100 hg38.150200.bed.split14863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14864 0 1 2 100 hg38.150200.bed.split14864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14865 0 1 2 100 hg38.150200.bed.split14865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14866 0 1 2 100 hg38.150200.bed.split14866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14867 0 1 2 100 hg38.150200.bed.split14867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14868 0 1 2 100 hg38.150200.bed.split14868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14869 0 1 2 100 hg38.150200.bed.split14869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1487 0 1 2 100 hg38.150200.bed.split1487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14870 0 1 2 100 hg38.150200.bed.split14870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14871 0 1 2 100 hg38.150200.bed.split14871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14872 0 1 2 100 hg38.150200.bed.split14872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14873 0 1 2 100 hg38.150200.bed.split14873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14874 0 1 2 100 hg38.150200.bed.split14874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14875 0 1 2 100 hg38.150200.bed.split14875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14876 0 1 2 100 hg38.150200.bed.split14876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14877 0 1 2 100 hg38.150200.bed.split14877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14878 0 1 2 100 hg38.150200.bed.split14878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14879 0 1 2 100 hg38.150200.bed.split14879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1488 0 1 2 100 hg38.150200.bed.split1488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14880 0 1 2 100 hg38.150200.bed.split14880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14881 0 1 2 100 hg38.150200.bed.split14881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14882 0 1 2 100 hg38.150200.bed.split14882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14883 0 1 2 100 hg38.150200.bed.split14883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14884 0 1 2 100 hg38.150200.bed.split14884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14885 0 1 2 100 hg38.150200.bed.split14885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14886 0 1 2 100 hg38.150200.bed.split14886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14887 0 1 2 100 hg38.150200.bed.split14887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14888 0 1 2 100 hg38.150200.bed.split14888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14889 0 1 2 100 hg38.150200.bed.split14889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1489 0 1 2 100 hg38.150200.bed.split1489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14890 0 1 2 100 hg38.150200.bed.split14890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14891 0 1 2 100 hg38.150200.bed.split14891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14892 0 1 2 100 hg38.150200.bed.split14892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14893 0 1 2 100 hg38.150200.bed.split14893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14894 0 1 2 100 hg38.150200.bed.split14894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14895 0 1 2 100 hg38.150200.bed.split14895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14896 0 1 2 100 hg38.150200.bed.split14896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14897 0 1 2 100 hg38.150200.bed.split14897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14898 0 1 2 100 hg38.150200.bed.split14898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14899 0 1 2 100 hg38.150200.bed.split14899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split149 0 1 2 100 hg38.150200.bed.split149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1490 0 1 2 100 hg38.150200.bed.split1490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14900 0 1 2 100 hg38.150200.bed.split14900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14901 0 1 2 100 hg38.150200.bed.split14901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14902 0 1 2 100 hg38.150200.bed.split14902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14903 0 1 2 100 hg38.150200.bed.split14903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14904 0 1 2 100 hg38.150200.bed.split14904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14905 0 1 2 100 hg38.150200.bed.split14905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14906 0 1 2 100 hg38.150200.bed.split14906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14907 0 1 2 100 hg38.150200.bed.split14907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14908 0 1 2 100 hg38.150200.bed.split14908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14909 0 1 2 100 hg38.150200.bed.split14909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1491 0 1 2 100 hg38.150200.bed.split1491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14910 0 1 2 100 hg38.150200.bed.split14910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14911 0 1 2 100 hg38.150200.bed.split14911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14912 0 1 2 100 hg38.150200.bed.split14912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14913 0 1 2 100 hg38.150200.bed.split14913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14914 0 1 2 100 hg38.150200.bed.split14914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14915 0 1 2 100 hg38.150200.bed.split14915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14916 0 1 2 100 hg38.150200.bed.split14916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14917 0 1 2 100 hg38.150200.bed.split14917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14918 0 1 2 100 hg38.150200.bed.split14918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14919 0 1 2 100 hg38.150200.bed.split14919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1492 0 1 2 100 hg38.150200.bed.split1492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14920 0 1 2 100 hg38.150200.bed.split14920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14921 0 1 2 100 hg38.150200.bed.split14921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14922 0 1 2 100 hg38.150200.bed.split14922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14923 0 1 2 100 hg38.150200.bed.split14923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14924 0 1 2 100 hg38.150200.bed.split14924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14925 0 1 2 100 hg38.150200.bed.split14925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14926 0 1 2 100 hg38.150200.bed.split14926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14927 0 1 2 100 hg38.150200.bed.split14927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14928 0 1 2 100 hg38.150200.bed.split14928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14929 0 1 2 100 hg38.150200.bed.split14929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1493 0 1 2 100 hg38.150200.bed.split1493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14930 0 1 2 100 hg38.150200.bed.split14930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14931 0 1 2 100 hg38.150200.bed.split14931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14932 0 1 2 100 hg38.150200.bed.split14932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14933 0 1 2 100 hg38.150200.bed.split14933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14934 0 1 2 100 hg38.150200.bed.split14934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14935 0 1 2 100 hg38.150200.bed.split14935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14936 0 1 2 100 hg38.150200.bed.split14936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14937 0 1 2 100 hg38.150200.bed.split14937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14938 0 1 2 100 hg38.150200.bed.split14938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14939 0 1 2 100 hg38.150200.bed.split14939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1494 0 1 2 100 hg38.150200.bed.split1494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14940 0 1 2 100 hg38.150200.bed.split14940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14941 0 1 2 100 hg38.150200.bed.split14941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14942 0 1 2 100 hg38.150200.bed.split14942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14943 0 1 2 100 hg38.150200.bed.split14943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14944 0 1 2 100 hg38.150200.bed.split14944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14945 0 1 2 100 hg38.150200.bed.split14945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14946 0 1 2 100 hg38.150200.bed.split14946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14947 0 1 2 100 hg38.150200.bed.split14947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14948 0 1 2 100 hg38.150200.bed.split14948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14949 0 1 2 100 hg38.150200.bed.split14949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1495 0 1 2 100 hg38.150200.bed.split1495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14950 0 1 2 100 hg38.150200.bed.split14950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14951 0 1 2 100 hg38.150200.bed.split14951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14952 0 1 2 100 hg38.150200.bed.split14952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14953 0 1 2 100 hg38.150200.bed.split14953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14954 0 1 2 100 hg38.150200.bed.split14954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14955 0 1 2 100 hg38.150200.bed.split14955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14956 0 1 2 100 hg38.150200.bed.split14956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14957 0 1 2 100 hg38.150200.bed.split14957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14958 0 1 2 100 hg38.150200.bed.split14958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14959 0 1 2 100 hg38.150200.bed.split14959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1496 0 1 2 100 hg38.150200.bed.split1496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14960 0 1 2 100 hg38.150200.bed.split14960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14961 0 1 2 100 hg38.150200.bed.split14961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14962 0 1 2 100 hg38.150200.bed.split14962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14963 0 1 2 100 hg38.150200.bed.split14963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14964 0 1 2 100 hg38.150200.bed.split14964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14965 0 1 2 100 hg38.150200.bed.split14965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14966 0 1 2 100 hg38.150200.bed.split14966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14967 0 1 2 100 hg38.150200.bed.split14967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14968 0 1 2 100 hg38.150200.bed.split14968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14969 0 1 2 100 hg38.150200.bed.split14969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1497 0 1 2 100 hg38.150200.bed.split1497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14970 0 1 2 100 hg38.150200.bed.split14970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14971 0 1 2 100 hg38.150200.bed.split14971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14972 0 1 2 100 hg38.150200.bed.split14972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14973 0 1 2 100 hg38.150200.bed.split14973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14974 0 1 2 100 hg38.150200.bed.split14974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14975 0 1 2 100 hg38.150200.bed.split14975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14976 0 1 2 100 hg38.150200.bed.split14976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14977 0 1 2 100 hg38.150200.bed.split14977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14978 0 1 2 100 hg38.150200.bed.split14978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14979 0 1 2 100 hg38.150200.bed.split14979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1498 0 1 2 100 hg38.150200.bed.split1498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14980 0 1 2 100 hg38.150200.bed.split14980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14981 0 1 2 100 hg38.150200.bed.split14981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14982 0 1 2 100 hg38.150200.bed.split14982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14983 0 1 2 100 hg38.150200.bed.split14983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14984 0 1 2 100 hg38.150200.bed.split14984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14985 0 1 2 100 hg38.150200.bed.split14985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14986 0 1 2 100 hg38.150200.bed.split14986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14987 0 1 2 100 hg38.150200.bed.split14987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14988 0 1 2 100 hg38.150200.bed.split14988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14989 0 1 2 100 hg38.150200.bed.split14989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1499 0 1 2 100 hg38.150200.bed.split1499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14990 0 1 2 100 hg38.150200.bed.split14990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14991 0 1 2 100 hg38.150200.bed.split14991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14992 0 1 2 100 hg38.150200.bed.split14992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14993 0 1 2 100 hg38.150200.bed.split14993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14994 0 1 2 100 hg38.150200.bed.split14994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14995 0 1 2 100 hg38.150200.bed.split14995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14996 0 1 2 100 hg38.150200.bed.split14996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14997 0 1 2 100 hg38.150200.bed.split14997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14998 0 1 2 100 hg38.150200.bed.split14998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split14999 0 1 2 100 hg38.150200.bed.split14999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15 0 1 2 100 hg38.150200.bed.split15.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split150 0 1 2 100 hg38.150200.bed.split150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1500 0 1 2 100 hg38.150200.bed.split1500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15000 0 1 2 100 hg38.150200.bed.split15000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15001 0 1 2 100 hg38.150200.bed.split15001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15002 0 1 2 100 hg38.150200.bed.split15002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15003 0 1 2 100 hg38.150200.bed.split15003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15004 0 1 2 100 hg38.150200.bed.split15004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15005 0 1 2 100 hg38.150200.bed.split15005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15006 0 1 2 100 hg38.150200.bed.split15006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15007 0 1 2 100 hg38.150200.bed.split15007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15008 0 1 2 100 hg38.150200.bed.split15008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15009 0 1 2 100 hg38.150200.bed.split15009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1501 0 1 2 100 hg38.150200.bed.split1501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15010 0 1 2 100 hg38.150200.bed.split15010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15011 0 1 2 100 hg38.150200.bed.split15011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15012 0 1 2 100 hg38.150200.bed.split15012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15013 0 1 2 100 hg38.150200.bed.split15013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15014 0 1 2 100 hg38.150200.bed.split15014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15015 0 1 2 100 hg38.150200.bed.split15015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15016 0 1 2 100 hg38.150200.bed.split15016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15017 0 1 2 100 hg38.150200.bed.split15017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15018 0 1 2 100 hg38.150200.bed.split15018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15019 0 1 2 100 hg38.150200.bed.split15019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1502 0 1 2 100 hg38.150200.bed.split1502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15020 0 1 2 100 hg38.150200.bed.split15020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15021 0 1 2 100 hg38.150200.bed.split15021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15022 0 1 2 100 hg38.150200.bed.split15022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15023 0 1 2 100 hg38.150200.bed.split15023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15024 0 1 2 100 hg38.150200.bed.split15024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15025 0 1 2 100 hg38.150200.bed.split15025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15026 0 1 2 100 hg38.150200.bed.split15026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15027 0 1 2 100 hg38.150200.bed.split15027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15028 0 1 2 100 hg38.150200.bed.split15028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15029 0 1 2 100 hg38.150200.bed.split15029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1503 0 1 2 100 hg38.150200.bed.split1503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15030 0 1 2 100 hg38.150200.bed.split15030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15031 0 1 2 100 hg38.150200.bed.split15031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15032 0 1 2 100 hg38.150200.bed.split15032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15033 0 1 2 100 hg38.150200.bed.split15033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15034 0 1 2 100 hg38.150200.bed.split15034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15035 0 1 2 100 hg38.150200.bed.split15035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15036 0 1 2 100 hg38.150200.bed.split15036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15037 0 1 2 100 hg38.150200.bed.split15037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15038 0 1 2 100 hg38.150200.bed.split15038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15039 0 1 2 100 hg38.150200.bed.split15039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1504 0 1 2 100 hg38.150200.bed.split1504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15040 0 1 2 100 hg38.150200.bed.split15040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15041 0 1 2 100 hg38.150200.bed.split15041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15042 0 1 2 100 hg38.150200.bed.split15042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15043 0 1 2 100 hg38.150200.bed.split15043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15044 0 1 2 100 hg38.150200.bed.split15044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15045 0 1 2 100 hg38.150200.bed.split15045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15046 0 1 2 100 hg38.150200.bed.split15046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15047 0 1 2 100 hg38.150200.bed.split15047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15048 0 1 2 100 hg38.150200.bed.split15048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15049 0 1 2 100 hg38.150200.bed.split15049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1505 0 1 2 100 hg38.150200.bed.split1505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15050 0 1 2 100 hg38.150200.bed.split15050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15051 0 1 2 100 hg38.150200.bed.split15051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15052 0 1 2 100 hg38.150200.bed.split15052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15053 0 1 2 100 hg38.150200.bed.split15053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15054 0 1 2 100 hg38.150200.bed.split15054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15055 0 1 2 100 hg38.150200.bed.split15055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15056 0 1 2 100 hg38.150200.bed.split15056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15057 0 1 2 100 hg38.150200.bed.split15057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15058 0 1 2 100 hg38.150200.bed.split15058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15059 0 1 2 100 hg38.150200.bed.split15059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1506 0 1 2 100 hg38.150200.bed.split1506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15060 0 1 2 100 hg38.150200.bed.split15060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15061 0 1 2 100 hg38.150200.bed.split15061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15062 0 1 2 100 hg38.150200.bed.split15062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15063 0 1 2 100 hg38.150200.bed.split15063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15064 0 1 2 100 hg38.150200.bed.split15064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15065 0 1 2 100 hg38.150200.bed.split15065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15066 0 1 2 100 hg38.150200.bed.split15066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15067 0 1 2 100 hg38.150200.bed.split15067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15068 0 1 2 100 hg38.150200.bed.split15068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15069 0 1 2 100 hg38.150200.bed.split15069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1507 0 1 2 100 hg38.150200.bed.split1507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15070 0 1 2 100 hg38.150200.bed.split15070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15071 0 1 2 100 hg38.150200.bed.split15071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15072 0 1 2 100 hg38.150200.bed.split15072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15073 0 1 2 100 hg38.150200.bed.split15073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15074 0 1 2 100 hg38.150200.bed.split15074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15075 0 1 2 100 hg38.150200.bed.split15075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15076 0 1 2 100 hg38.150200.bed.split15076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15077 0 1 2 100 hg38.150200.bed.split15077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15078 0 1 2 100 hg38.150200.bed.split15078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15079 0 1 2 100 hg38.150200.bed.split15079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1508 0 1 2 100 hg38.150200.bed.split1508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15080 0 1 2 100 hg38.150200.bed.split15080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15081 0 1 2 100 hg38.150200.bed.split15081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15082 0 1 2 100 hg38.150200.bed.split15082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15083 0 1 2 100 hg38.150200.bed.split15083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15084 0 1 2 100 hg38.150200.bed.split15084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15085 0 1 2 100 hg38.150200.bed.split15085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15086 0 1 2 100 hg38.150200.bed.split15086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15087 0 1 2 100 hg38.150200.bed.split15087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15088 0 1 2 100 hg38.150200.bed.split15088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15089 0 1 2 100 hg38.150200.bed.split15089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1509 0 1 2 100 hg38.150200.bed.split1509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15090 0 1 2 100 hg38.150200.bed.split15090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15091 0 1 2 100 hg38.150200.bed.split15091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15092 0 1 2 100 hg38.150200.bed.split15092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15093 0 1 2 100 hg38.150200.bed.split15093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15094 0 1 2 100 hg38.150200.bed.split15094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15095 0 1 2 100 hg38.150200.bed.split15095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15096 0 1 2 100 hg38.150200.bed.split15096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15097 0 1 2 100 hg38.150200.bed.split15097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15098 0 1 2 100 hg38.150200.bed.split15098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15099 0 1 2 100 hg38.150200.bed.split15099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split151 0 1 2 100 hg38.150200.bed.split151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1510 0 1 2 100 hg38.150200.bed.split1510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15100 0 1 2 100 hg38.150200.bed.split15100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15101 0 1 2 100 hg38.150200.bed.split15101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15102 0 1 2 100 hg38.150200.bed.split15102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15103 0 1 2 100 hg38.150200.bed.split15103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15104 0 1 2 100 hg38.150200.bed.split15104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15105 0 1 2 100 hg38.150200.bed.split15105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15106 0 1 2 100 hg38.150200.bed.split15106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15107 0 1 2 100 hg38.150200.bed.split15107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15108 0 1 2 100 hg38.150200.bed.split15108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15109 0 1 2 100 hg38.150200.bed.split15109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1511 0 1 2 100 hg38.150200.bed.split1511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15110 0 1 2 100 hg38.150200.bed.split15110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15111 0 1 2 100 hg38.150200.bed.split15111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15112 0 1 2 100 hg38.150200.bed.split15112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15113 0 1 2 100 hg38.150200.bed.split15113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15114 0 1 2 100 hg38.150200.bed.split15114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15115 0 1 2 100 hg38.150200.bed.split15115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15116 0 1 2 100 hg38.150200.bed.split15116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15117 0 1 2 100 hg38.150200.bed.split15117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15118 0 1 2 100 hg38.150200.bed.split15118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15119 0 1 2 100 hg38.150200.bed.split15119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1512 0 1 2 100 hg38.150200.bed.split1512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15120 0 1 2 100 hg38.150200.bed.split15120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15121 0 1 2 100 hg38.150200.bed.split15121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15122 0 1 2 100 hg38.150200.bed.split15122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15123 0 1 2 100 hg38.150200.bed.split15123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15124 0 1 2 100 hg38.150200.bed.split15124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15125 0 1 2 100 hg38.150200.bed.split15125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15126 0 1 2 100 hg38.150200.bed.split15126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15127 0 1 2 100 hg38.150200.bed.split15127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15128 0 1 2 100 hg38.150200.bed.split15128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15129 0 1 2 100 hg38.150200.bed.split15129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1513 0 1 2 100 hg38.150200.bed.split1513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15130 0 1 2 100 hg38.150200.bed.split15130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15131 0 1 2 100 hg38.150200.bed.split15131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15132 0 1 2 100 hg38.150200.bed.split15132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15133 0 1 2 100 hg38.150200.bed.split15133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15134 0 1 2 100 hg38.150200.bed.split15134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15135 0 1 2 100 hg38.150200.bed.split15135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15136 0 1 2 100 hg38.150200.bed.split15136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15137 0 1 2 100 hg38.150200.bed.split15137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15138 0 1 2 100 hg38.150200.bed.split15138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15139 0 1 2 100 hg38.150200.bed.split15139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1514 0 1 2 100 hg38.150200.bed.split1514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15140 0 1 2 100 hg38.150200.bed.split15140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15141 0 1 2 100 hg38.150200.bed.split15141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15142 0 1 2 100 hg38.150200.bed.split15142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15143 0 1 2 100 hg38.150200.bed.split15143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15144 0 1 2 100 hg38.150200.bed.split15144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15145 0 1 2 100 hg38.150200.bed.split15145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15146 0 1 2 100 hg38.150200.bed.split15146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15147 0 1 2 100 hg38.150200.bed.split15147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15148 0 1 2 100 hg38.150200.bed.split15148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15149 0 1 2 100 hg38.150200.bed.split15149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1515 0 1 2 100 hg38.150200.bed.split1515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15150 0 1 2 100 hg38.150200.bed.split15150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15151 0 1 2 100 hg38.150200.bed.split15151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15152 0 1 2 100 hg38.150200.bed.split15152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15153 0 1 2 100 hg38.150200.bed.split15153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15154 0 1 2 100 hg38.150200.bed.split15154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15155 0 1 2 100 hg38.150200.bed.split15155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15156 0 1 2 100 hg38.150200.bed.split15156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15157 0 1 2 100 hg38.150200.bed.split15157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15158 0 1 2 100 hg38.150200.bed.split15158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15159 0 1 2 100 hg38.150200.bed.split15159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1516 0 1 2 100 hg38.150200.bed.split1516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15160 0 1 2 100 hg38.150200.bed.split15160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15161 0 1 2 100 hg38.150200.bed.split15161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15162 0 1 2 100 hg38.150200.bed.split15162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15163 0 1 2 100 hg38.150200.bed.split15163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15164 0 1 2 100 hg38.150200.bed.split15164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15165 0 1 2 100 hg38.150200.bed.split15165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15166 0 1 2 100 hg38.150200.bed.split15166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15167 0 1 2 100 hg38.150200.bed.split15167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15168 0 1 2 100 hg38.150200.bed.split15168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15169 0 1 2 100 hg38.150200.bed.split15169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1517 0 1 2 100 hg38.150200.bed.split1517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15170 0 1 2 100 hg38.150200.bed.split15170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15171 0 1 2 100 hg38.150200.bed.split15171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15172 0 1 2 100 hg38.150200.bed.split15172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15173 0 1 2 100 hg38.150200.bed.split15173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15174 0 1 2 100 hg38.150200.bed.split15174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15175 0 1 2 100 hg38.150200.bed.split15175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15176 0 1 2 100 hg38.150200.bed.split15176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15177 0 1 2 100 hg38.150200.bed.split15177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15178 0 1 2 100 hg38.150200.bed.split15178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15179 0 1 2 100 hg38.150200.bed.split15179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1518 0 1 2 100 hg38.150200.bed.split1518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15180 0 1 2 100 hg38.150200.bed.split15180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15181 0 1 2 100 hg38.150200.bed.split15181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15182 0 1 2 100 hg38.150200.bed.split15182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15183 0 1 2 100 hg38.150200.bed.split15183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15184 0 1 2 100 hg38.150200.bed.split15184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15185 0 1 2 100 hg38.150200.bed.split15185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15186 0 1 2 100 hg38.150200.bed.split15186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15187 0 1 2 100 hg38.150200.bed.split15187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15188 0 1 2 100 hg38.150200.bed.split15188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15189 0 1 2 100 hg38.150200.bed.split15189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1519 0 1 2 100 hg38.150200.bed.split1519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15190 0 1 2 100 hg38.150200.bed.split15190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15191 0 1 2 100 hg38.150200.bed.split15191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15192 0 1 2 100 hg38.150200.bed.split15192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15193 0 1 2 100 hg38.150200.bed.split15193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15194 0 1 2 100 hg38.150200.bed.split15194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15195 0 1 2 100 hg38.150200.bed.split15195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15196 0 1 2 100 hg38.150200.bed.split15196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15197 0 1 2 100 hg38.150200.bed.split15197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15198 0 1 2 100 hg38.150200.bed.split15198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15199 0 1 2 100 hg38.150200.bed.split15199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split152 0 1 2 100 hg38.150200.bed.split152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1520 0 1 2 100 hg38.150200.bed.split1520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15200 0 1 2 100 hg38.150200.bed.split15200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15201 0 1 2 100 hg38.150200.bed.split15201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15202 0 1 2 100 hg38.150200.bed.split15202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15203 0 1 2 100 hg38.150200.bed.split15203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15204 0 1 2 100 hg38.150200.bed.split15204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15205 0 1 2 100 hg38.150200.bed.split15205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15206 0 1 2 100 hg38.150200.bed.split15206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15207 0 1 2 100 hg38.150200.bed.split15207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15208 0 1 2 100 hg38.150200.bed.split15208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15209 0 1 2 100 hg38.150200.bed.split15209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1521 0 1 2 100 hg38.150200.bed.split1521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15210 0 1 2 100 hg38.150200.bed.split15210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15211 0 1 2 100 hg38.150200.bed.split15211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15212 0 1 2 100 hg38.150200.bed.split15212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15213 0 1 2 100 hg38.150200.bed.split15213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15214 0 1 2 100 hg38.150200.bed.split15214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15215 0 1 2 100 hg38.150200.bed.split15215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15216 0 1 2 100 hg38.150200.bed.split15216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15217 0 1 2 100 hg38.150200.bed.split15217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15218 0 1 2 100 hg38.150200.bed.split15218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15219 0 1 2 100 hg38.150200.bed.split15219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1522 0 1 2 100 hg38.150200.bed.split1522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15220 0 1 2 100 hg38.150200.bed.split15220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15221 0 1 2 100 hg38.150200.bed.split15221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15222 0 1 2 100 hg38.150200.bed.split15222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15223 0 1 2 100 hg38.150200.bed.split15223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15224 0 1 2 100 hg38.150200.bed.split15224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15225 0 1 2 100 hg38.150200.bed.split15225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15226 0 1 2 100 hg38.150200.bed.split15226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15227 0 1 2 100 hg38.150200.bed.split15227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15228 0 1 2 100 hg38.150200.bed.split15228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15229 0 1 2 100 hg38.150200.bed.split15229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1523 0 1 2 100 hg38.150200.bed.split1523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15230 0 1 2 100 hg38.150200.bed.split15230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15231 0 1 2 100 hg38.150200.bed.split15231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15232 0 1 2 100 hg38.150200.bed.split15232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15233 0 1 2 100 hg38.150200.bed.split15233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15234 0 1 2 100 hg38.150200.bed.split15234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15235 0 1 2 100 hg38.150200.bed.split15235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15236 0 1 2 100 hg38.150200.bed.split15236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15237 0 1 2 100 hg38.150200.bed.split15237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15238 0 1 2 100 hg38.150200.bed.split15238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15239 0 1 2 100 hg38.150200.bed.split15239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1524 0 1 2 100 hg38.150200.bed.split1524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15240 0 1 2 100 hg38.150200.bed.split15240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15241 0 1 2 100 hg38.150200.bed.split15241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15242 0 1 2 100 hg38.150200.bed.split15242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15243 0 1 2 100 hg38.150200.bed.split15243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15244 0 1 2 100 hg38.150200.bed.split15244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15245 0 1 2 100 hg38.150200.bed.split15245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15246 0 1 2 100 hg38.150200.bed.split15246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15247 0 1 2 100 hg38.150200.bed.split15247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15248 0 1 2 100 hg38.150200.bed.split15248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15249 0 1 2 100 hg38.150200.bed.split15249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1525 0 1 2 100 hg38.150200.bed.split1525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15250 0 1 2 100 hg38.150200.bed.split15250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15251 0 1 2 100 hg38.150200.bed.split15251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15252 0 1 2 100 hg38.150200.bed.split15252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15253 0 1 2 100 hg38.150200.bed.split15253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15254 0 1 2 100 hg38.150200.bed.split15254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15255 0 1 2 100 hg38.150200.bed.split15255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15256 0 1 2 100 hg38.150200.bed.split15256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15257 0 1 2 100 hg38.150200.bed.split15257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15258 0 1 2 100 hg38.150200.bed.split15258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15259 0 1 2 100 hg38.150200.bed.split15259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1526 0 1 2 100 hg38.150200.bed.split1526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15260 0 1 2 100 hg38.150200.bed.split15260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15261 0 1 2 100 hg38.150200.bed.split15261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15262 0 1 2 100 hg38.150200.bed.split15262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15263 0 1 2 100 hg38.150200.bed.split15263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15264 0 1 2 100 hg38.150200.bed.split15264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15265 0 1 2 100 hg38.150200.bed.split15265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15266 0 1 2 100 hg38.150200.bed.split15266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15267 0 1 2 100 hg38.150200.bed.split15267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15268 0 1 2 100 hg38.150200.bed.split15268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15269 0 1 2 100 hg38.150200.bed.split15269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1527 0 1 2 100 hg38.150200.bed.split1527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15270 0 1 2 100 hg38.150200.bed.split15270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15271 0 1 2 100 hg38.150200.bed.split15271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15272 0 1 2 100 hg38.150200.bed.split15272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15273 0 1 2 100 hg38.150200.bed.split15273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15274 0 1 2 100 hg38.150200.bed.split15274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15275 0 1 2 100 hg38.150200.bed.split15275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15276 0 1 2 100 hg38.150200.bed.split15276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15277 0 1 2 100 hg38.150200.bed.split15277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15278 0 1 2 100 hg38.150200.bed.split15278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15279 0 1 2 100 hg38.150200.bed.split15279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1528 0 1 2 100 hg38.150200.bed.split1528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15280 0 1 2 100 hg38.150200.bed.split15280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15281 0 1 2 100 hg38.150200.bed.split15281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15282 0 1 2 100 hg38.150200.bed.split15282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15283 0 1 2 100 hg38.150200.bed.split15283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15284 0 1 2 100 hg38.150200.bed.split15284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15285 0 1 2 100 hg38.150200.bed.split15285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15286 0 1 2 100 hg38.150200.bed.split15286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15287 0 1 2 100 hg38.150200.bed.split15287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15288 0 1 2 100 hg38.150200.bed.split15288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15289 0 1 2 100 hg38.150200.bed.split15289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1529 0 1 2 100 hg38.150200.bed.split1529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15290 0 1 2 100 hg38.150200.bed.split15290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15291 0 1 2 100 hg38.150200.bed.split15291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15292 0 1 2 100 hg38.150200.bed.split15292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15293 0 1 2 100 hg38.150200.bed.split15293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15294 0 1 2 100 hg38.150200.bed.split15294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15295 0 1 2 100 hg38.150200.bed.split15295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15296 0 1 2 100 hg38.150200.bed.split15296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15297 0 1 2 100 hg38.150200.bed.split15297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15298 0 1 2 100 hg38.150200.bed.split15298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15299 0 1 2 100 hg38.150200.bed.split15299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split153 0 1 2 100 hg38.150200.bed.split153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1530 0 1 2 100 hg38.150200.bed.split1530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15300 0 1 2 100 hg38.150200.bed.split15300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15301 0 1 2 100 hg38.150200.bed.split15301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15302 0 1 2 100 hg38.150200.bed.split15302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15303 0 1 2 100 hg38.150200.bed.split15303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15304 0 1 2 100 hg38.150200.bed.split15304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15305 0 1 2 100 hg38.150200.bed.split15305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15306 0 1 2 100 hg38.150200.bed.split15306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15307 0 1 2 100 hg38.150200.bed.split15307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15308 0 1 2 100 hg38.150200.bed.split15308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15309 0 1 2 100 hg38.150200.bed.split15309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1531 0 1 2 100 hg38.150200.bed.split1531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15310 0 1 2 100 hg38.150200.bed.split15310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15311 0 1 2 100 hg38.150200.bed.split15311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15312 0 1 2 100 hg38.150200.bed.split15312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15313 0 1 2 100 hg38.150200.bed.split15313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15314 0 1 2 100 hg38.150200.bed.split15314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15315 0 1 2 100 hg38.150200.bed.split15315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15316 0 1 2 100 hg38.150200.bed.split15316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15317 0 1 2 100 hg38.150200.bed.split15317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15318 0 1 2 100 hg38.150200.bed.split15318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15319 0 1 2 100 hg38.150200.bed.split15319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1532 0 1 2 100 hg38.150200.bed.split1532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15320 0 1 2 100 hg38.150200.bed.split15320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15321 0 1 2 100 hg38.150200.bed.split15321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15322 0 1 2 100 hg38.150200.bed.split15322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15323 0 1 2 100 hg38.150200.bed.split15323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15324 0 1 2 100 hg38.150200.bed.split15324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15325 0 1 2 100 hg38.150200.bed.split15325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15326 0 1 2 100 hg38.150200.bed.split15326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15327 0 1 2 100 hg38.150200.bed.split15327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15328 0 1 2 100 hg38.150200.bed.split15328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15329 0 1 2 100 hg38.150200.bed.split15329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1533 0 1 2 100 hg38.150200.bed.split1533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15330 0 1 2 100 hg38.150200.bed.split15330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15331 0 1 2 100 hg38.150200.bed.split15331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15332 0 1 2 100 hg38.150200.bed.split15332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15333 0 1 2 100 hg38.150200.bed.split15333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15334 0 1 2 100 hg38.150200.bed.split15334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15335 0 1 2 100 hg38.150200.bed.split15335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15336 0 1 2 100 hg38.150200.bed.split15336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15337 0 1 2 100 hg38.150200.bed.split15337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15338 0 1 2 100 hg38.150200.bed.split15338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15339 0 1 2 100 hg38.150200.bed.split15339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1534 0 1 2 100 hg38.150200.bed.split1534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15340 0 1 2 100 hg38.150200.bed.split15340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15341 0 1 2 100 hg38.150200.bed.split15341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15342 0 1 2 100 hg38.150200.bed.split15342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15343 0 1 2 100 hg38.150200.bed.split15343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15344 0 1 2 100 hg38.150200.bed.split15344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15345 0 1 2 100 hg38.150200.bed.split15345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15346 0 1 2 100 hg38.150200.bed.split15346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15347 0 1 2 100 hg38.150200.bed.split15347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15348 0 1 2 100 hg38.150200.bed.split15348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15349 0 1 2 100 hg38.150200.bed.split15349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1535 0 1 2 100 hg38.150200.bed.split1535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15350 0 1 2 100 hg38.150200.bed.split15350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15351 0 1 2 100 hg38.150200.bed.split15351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15352 0 1 2 100 hg38.150200.bed.split15352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15353 0 1 2 100 hg38.150200.bed.split15353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15354 0 1 2 100 hg38.150200.bed.split15354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15355 0 1 2 100 hg38.150200.bed.split15355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15356 0 1 2 100 hg38.150200.bed.split15356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15357 0 1 2 100 hg38.150200.bed.split15357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15358 0 1 2 100 hg38.150200.bed.split15358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15359 0 1 2 100 hg38.150200.bed.split15359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1536 0 1 2 100 hg38.150200.bed.split1536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15360 0 1 2 100 hg38.150200.bed.split15360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15361 0 1 2 100 hg38.150200.bed.split15361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15362 0 1 2 100 hg38.150200.bed.split15362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15363 0 1 2 100 hg38.150200.bed.split15363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15364 0 1 2 100 hg38.150200.bed.split15364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15365 0 1 2 100 hg38.150200.bed.split15365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15366 0 1 2 100 hg38.150200.bed.split15366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15367 0 1 2 100 hg38.150200.bed.split15367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15368 0 1 2 100 hg38.150200.bed.split15368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15369 0 1 2 100 hg38.150200.bed.split15369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1537 0 1 2 100 hg38.150200.bed.split1537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15370 0 1 2 100 hg38.150200.bed.split15370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15371 0 1 2 100 hg38.150200.bed.split15371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15372 0 1 2 100 hg38.150200.bed.split15372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15373 0 1 2 100 hg38.150200.bed.split15373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15374 0 1 2 100 hg38.150200.bed.split15374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15375 0 1 2 100 hg38.150200.bed.split15375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15376 0 1 2 100 hg38.150200.bed.split15376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15377 0 1 2 100 hg38.150200.bed.split15377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15378 0 1 2 100 hg38.150200.bed.split15378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15379 0 1 2 100 hg38.150200.bed.split15379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1538 0 1 2 100 hg38.150200.bed.split1538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15380 0 1 2 100 hg38.150200.bed.split15380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15381 0 1 2 100 hg38.150200.bed.split15381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15382 0 1 2 100 hg38.150200.bed.split15382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15383 0 1 2 100 hg38.150200.bed.split15383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15384 0 1 2 100 hg38.150200.bed.split15384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15385 0 1 2 100 hg38.150200.bed.split15385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15386 0 1 2 100 hg38.150200.bed.split15386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15387 0 1 2 100 hg38.150200.bed.split15387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15388 0 1 2 100 hg38.150200.bed.split15388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15389 0 1 2 100 hg38.150200.bed.split15389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1539 0 1 2 100 hg38.150200.bed.split1539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15390 0 1 2 100 hg38.150200.bed.split15390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15391 0 1 2 100 hg38.150200.bed.split15391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15392 0 1 2 100 hg38.150200.bed.split15392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15393 0 1 2 100 hg38.150200.bed.split15393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15394 0 1 2 100 hg38.150200.bed.split15394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15395 0 1 2 100 hg38.150200.bed.split15395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15396 0 1 2 100 hg38.150200.bed.split15396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15397 0 1 2 100 hg38.150200.bed.split15397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15398 0 1 2 100 hg38.150200.bed.split15398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15399 0 1 2 100 hg38.150200.bed.split15399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split154 0 1 2 100 hg38.150200.bed.split154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1540 0 1 2 100 hg38.150200.bed.split1540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15400 0 1 2 100 hg38.150200.bed.split15400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15401 0 1 2 100 hg38.150200.bed.split15401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15402 0 1 2 100 hg38.150200.bed.split15402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15403 0 1 2 100 hg38.150200.bed.split15403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15404 0 1 2 100 hg38.150200.bed.split15404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15405 0 1 2 100 hg38.150200.bed.split15405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15406 0 1 2 100 hg38.150200.bed.split15406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15407 0 1 2 100 hg38.150200.bed.split15407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15408 0 1 2 100 hg38.150200.bed.split15408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15409 0 1 2 100 hg38.150200.bed.split15409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1541 0 1 2 100 hg38.150200.bed.split1541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15410 0 1 2 100 hg38.150200.bed.split15410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15411 0 1 2 100 hg38.150200.bed.split15411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15412 0 1 2 100 hg38.150200.bed.split15412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15413 0 1 2 100 hg38.150200.bed.split15413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15414 0 1 2 100 hg38.150200.bed.split15414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15415 0 1 2 100 hg38.150200.bed.split15415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15416 0 1 2 100 hg38.150200.bed.split15416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15417 0 1 2 100 hg38.150200.bed.split15417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15418 0 1 2 100 hg38.150200.bed.split15418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15419 0 1 2 100 hg38.150200.bed.split15419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1542 0 1 2 100 hg38.150200.bed.split1542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15420 0 1 2 100 hg38.150200.bed.split15420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15421 0 1 2 100 hg38.150200.bed.split15421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15422 0 1 2 100 hg38.150200.bed.split15422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15423 0 1 2 100 hg38.150200.bed.split15423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15424 0 1 2 100 hg38.150200.bed.split15424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15425 0 1 2 100 hg38.150200.bed.split15425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15426 0 1 2 100 hg38.150200.bed.split15426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15427 0 1 2 100 hg38.150200.bed.split15427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15428 0 1 2 100 hg38.150200.bed.split15428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15429 0 1 2 100 hg38.150200.bed.split15429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1543 0 1 2 100 hg38.150200.bed.split1543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15430 0 1 2 100 hg38.150200.bed.split15430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15431 0 1 2 100 hg38.150200.bed.split15431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15432 0 1 2 100 hg38.150200.bed.split15432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15433 0 1 2 100 hg38.150200.bed.split15433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15434 0 1 2 100 hg38.150200.bed.split15434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15435 0 1 2 100 hg38.150200.bed.split15435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15436 0 1 2 100 hg38.150200.bed.split15436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15437 0 1 2 100 hg38.150200.bed.split15437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15438 0 1 2 100 hg38.150200.bed.split15438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15439 0 1 2 100 hg38.150200.bed.split15439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1544 0 1 2 100 hg38.150200.bed.split1544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15440 0 1 2 100 hg38.150200.bed.split15440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15441 0 1 2 100 hg38.150200.bed.split15441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15442 0 1 2 100 hg38.150200.bed.split15442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15443 0 1 2 100 hg38.150200.bed.split15443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15444 0 1 2 100 hg38.150200.bed.split15444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15445 0 1 2 100 hg38.150200.bed.split15445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15446 0 1 2 100 hg38.150200.bed.split15446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15447 0 1 2 100 hg38.150200.bed.split15447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15448 0 1 2 100 hg38.150200.bed.split15448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15449 0 1 2 100 hg38.150200.bed.split15449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1545 0 1 2 100 hg38.150200.bed.split1545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15450 0 1 2 100 hg38.150200.bed.split15450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15451 0 1 2 100 hg38.150200.bed.split15451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15452 0 1 2 100 hg38.150200.bed.split15452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15453 0 1 2 100 hg38.150200.bed.split15453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15454 0 1 2 100 hg38.150200.bed.split15454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15455 0 1 2 100 hg38.150200.bed.split15455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15456 0 1 2 100 hg38.150200.bed.split15456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15457 0 1 2 100 hg38.150200.bed.split15457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15458 0 1 2 100 hg38.150200.bed.split15458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15459 0 1 2 100 hg38.150200.bed.split15459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1546 0 1 2 100 hg38.150200.bed.split1546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15460 0 1 2 100 hg38.150200.bed.split15460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15461 0 1 2 100 hg38.150200.bed.split15461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15462 0 1 2 100 hg38.150200.bed.split15462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15463 0 1 2 100 hg38.150200.bed.split15463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15464 0 1 2 100 hg38.150200.bed.split15464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15465 0 1 2 100 hg38.150200.bed.split15465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15466 0 1 2 100 hg38.150200.bed.split15466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15467 0 1 2 100 hg38.150200.bed.split15467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15468 0 1 2 100 hg38.150200.bed.split15468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15469 0 1 2 100 hg38.150200.bed.split15469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1547 0 1 2 100 hg38.150200.bed.split1547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15470 0 1 2 100 hg38.150200.bed.split15470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15471 0 1 2 100 hg38.150200.bed.split15471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15472 0 1 2 100 hg38.150200.bed.split15472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15473 0 1 2 100 hg38.150200.bed.split15473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15474 0 1 2 100 hg38.150200.bed.split15474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15475 0 1 2 100 hg38.150200.bed.split15475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15476 0 1 2 100 hg38.150200.bed.split15476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15477 0 1 2 100 hg38.150200.bed.split15477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15478 0 1 2 100 hg38.150200.bed.split15478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15479 0 1 2 100 hg38.150200.bed.split15479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1548 0 1 2 100 hg38.150200.bed.split1548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15480 0 1 2 100 hg38.150200.bed.split15480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15481 0 1 2 100 hg38.150200.bed.split15481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15482 0 1 2 100 hg38.150200.bed.split15482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15483 0 1 2 100 hg38.150200.bed.split15483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15484 0 1 2 100 hg38.150200.bed.split15484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15485 0 1 2 100 hg38.150200.bed.split15485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15486 0 1 2 100 hg38.150200.bed.split15486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15487 0 1 2 100 hg38.150200.bed.split15487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15488 0 1 2 100 hg38.150200.bed.split15488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15489 0 1 2 100 hg38.150200.bed.split15489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1549 0 1 2 100 hg38.150200.bed.split1549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15490 0 1 2 100 hg38.150200.bed.split15490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15491 0 1 2 100 hg38.150200.bed.split15491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15492 0 1 2 100 hg38.150200.bed.split15492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15493 0 1 2 100 hg38.150200.bed.split15493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15494 0 1 2 100 hg38.150200.bed.split15494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15495 0 1 2 100 hg38.150200.bed.split15495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15496 0 1 2 100 hg38.150200.bed.split15496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15497 0 1 2 100 hg38.150200.bed.split15497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15498 0 1 2 100 hg38.150200.bed.split15498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15499 0 1 2 100 hg38.150200.bed.split15499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split155 0 1 2 100 hg38.150200.bed.split155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1550 0 1 2 100 hg38.150200.bed.split1550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15500 0 1 2 100 hg38.150200.bed.split15500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15501 0 1 2 100 hg38.150200.bed.split15501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15502 0 1 2 100 hg38.150200.bed.split15502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15503 0 1 2 100 hg38.150200.bed.split15503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15504 0 1 2 100 hg38.150200.bed.split15504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15505 0 1 2 100 hg38.150200.bed.split15505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15506 0 1 2 100 hg38.150200.bed.split15506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15507 0 1 2 100 hg38.150200.bed.split15507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15508 0 1 2 100 hg38.150200.bed.split15508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15509 0 1 2 100 hg38.150200.bed.split15509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1551 0 1 2 100 hg38.150200.bed.split1551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15510 0 1 2 100 hg38.150200.bed.split15510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15511 0 1 2 100 hg38.150200.bed.split15511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15512 0 1 2 100 hg38.150200.bed.split15512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15513 0 1 2 100 hg38.150200.bed.split15513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15514 0 1 2 100 hg38.150200.bed.split15514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15515 0 1 2 100 hg38.150200.bed.split15515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15516 0 1 2 100 hg38.150200.bed.split15516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15517 0 1 2 100 hg38.150200.bed.split15517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15518 0 1 2 100 hg38.150200.bed.split15518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15519 0 1 2 100 hg38.150200.bed.split15519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1552 0 1 2 100 hg38.150200.bed.split1552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15520 0 1 2 100 hg38.150200.bed.split15520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15521 0 1 2 100 hg38.150200.bed.split15521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15522 0 1 2 100 hg38.150200.bed.split15522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15523 0 1 2 100 hg38.150200.bed.split15523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15524 0 1 2 100 hg38.150200.bed.split15524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15525 0 1 2 100 hg38.150200.bed.split15525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15526 0 1 2 100 hg38.150200.bed.split15526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15527 0 1 2 100 hg38.150200.bed.split15527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15528 0 1 2 100 hg38.150200.bed.split15528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15529 0 1 2 100 hg38.150200.bed.split15529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1553 0 1 2 100 hg38.150200.bed.split1553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15530 0 1 2 100 hg38.150200.bed.split15530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15531 0 1 2 100 hg38.150200.bed.split15531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15532 0 1 2 100 hg38.150200.bed.split15532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15533 0 1 2 100 hg38.150200.bed.split15533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15534 0 1 2 100 hg38.150200.bed.split15534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15535 0 1 2 100 hg38.150200.bed.split15535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15536 0 1 2 100 hg38.150200.bed.split15536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15537 0 1 2 100 hg38.150200.bed.split15537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15538 0 1 2 100 hg38.150200.bed.split15538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15539 0 1 2 100 hg38.150200.bed.split15539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1554 0 1 2 100 hg38.150200.bed.split1554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15540 0 1 2 100 hg38.150200.bed.split15540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15541 0 1 2 100 hg38.150200.bed.split15541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15542 0 1 2 100 hg38.150200.bed.split15542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15543 0 1 2 100 hg38.150200.bed.split15543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15544 0 1 2 100 hg38.150200.bed.split15544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15545 0 1 2 100 hg38.150200.bed.split15545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15546 0 1 2 100 hg38.150200.bed.split15546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15547 0 1 2 100 hg38.150200.bed.split15547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15548 0 1 2 100 hg38.150200.bed.split15548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15549 0 1 2 100 hg38.150200.bed.split15549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1555 0 1 2 100 hg38.150200.bed.split1555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15550 0 1 2 100 hg38.150200.bed.split15550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15551 0 1 2 100 hg38.150200.bed.split15551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15552 0 1 2 100 hg38.150200.bed.split15552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15553 0 1 2 100 hg38.150200.bed.split15553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15554 0 1 2 100 hg38.150200.bed.split15554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15555 0 1 2 100 hg38.150200.bed.split15555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15556 0 1 2 100 hg38.150200.bed.split15556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15557 0 1 2 100 hg38.150200.bed.split15557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15558 0 1 2 100 hg38.150200.bed.split15558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15559 0 1 2 100 hg38.150200.bed.split15559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1556 0 1 2 100 hg38.150200.bed.split1556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15560 0 1 2 100 hg38.150200.bed.split15560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15561 0 1 2 100 hg38.150200.bed.split15561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15562 0 1 2 100 hg38.150200.bed.split15562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15563 0 1 2 100 hg38.150200.bed.split15563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15564 0 1 2 100 hg38.150200.bed.split15564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15565 0 1 2 100 hg38.150200.bed.split15565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15566 0 1 2 100 hg38.150200.bed.split15566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15567 0 1 2 100 hg38.150200.bed.split15567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15568 0 1 2 100 hg38.150200.bed.split15568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15569 0 1 2 100 hg38.150200.bed.split15569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1557 0 1 2 100 hg38.150200.bed.split1557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15570 0 1 2 100 hg38.150200.bed.split15570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15571 0 1 2 100 hg38.150200.bed.split15571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15572 0 1 2 100 hg38.150200.bed.split15572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15573 0 1 2 100 hg38.150200.bed.split15573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15574 0 1 2 100 hg38.150200.bed.split15574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15575 0 1 2 100 hg38.150200.bed.split15575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15576 0 1 2 100 hg38.150200.bed.split15576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15577 0 1 2 100 hg38.150200.bed.split15577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15578 0 1 2 100 hg38.150200.bed.split15578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15579 0 1 2 100 hg38.150200.bed.split15579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1558 0 1 2 100 hg38.150200.bed.split1558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15580 0 1 2 100 hg38.150200.bed.split15580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15581 0 1 2 100 hg38.150200.bed.split15581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15582 0 1 2 100 hg38.150200.bed.split15582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15583 0 1 2 100 hg38.150200.bed.split15583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15584 0 1 2 100 hg38.150200.bed.split15584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15585 0 1 2 100 hg38.150200.bed.split15585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15586 0 1 2 100 hg38.150200.bed.split15586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15587 0 1 2 100 hg38.150200.bed.split15587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15588 0 1 2 100 hg38.150200.bed.split15588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15589 0 1 2 100 hg38.150200.bed.split15589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1559 0 1 2 100 hg38.150200.bed.split1559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15590 0 1 2 100 hg38.150200.bed.split15590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15591 0 1 2 100 hg38.150200.bed.split15591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15592 0 1 2 100 hg38.150200.bed.split15592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15593 0 1 2 100 hg38.150200.bed.split15593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15594 0 1 2 100 hg38.150200.bed.split15594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15595 0 1 2 100 hg38.150200.bed.split15595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15596 0 1 2 100 hg38.150200.bed.split15596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15597 0 1 2 100 hg38.150200.bed.split15597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15598 0 1 2 100 hg38.150200.bed.split15598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15599 0 1 2 100 hg38.150200.bed.split15599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split156 0 1 2 100 hg38.150200.bed.split156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1560 0 1 2 100 hg38.150200.bed.split1560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15600 0 1 2 100 hg38.150200.bed.split15600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15601 0 1 2 100 hg38.150200.bed.split15601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15602 0 1 2 100 hg38.150200.bed.split15602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15603 0 1 2 100 hg38.150200.bed.split15603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15604 0 1 2 100 hg38.150200.bed.split15604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15605 0 1 2 100 hg38.150200.bed.split15605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15606 0 1 2 100 hg38.150200.bed.split15606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15607 0 1 2 100 hg38.150200.bed.split15607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15608 0 1 2 100 hg38.150200.bed.split15608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15609 0 1 2 100 hg38.150200.bed.split15609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1561 0 1 2 100 hg38.150200.bed.split1561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15610 0 1 2 100 hg38.150200.bed.split15610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15611 0 1 2 100 hg38.150200.bed.split15611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15612 0 1 2 100 hg38.150200.bed.split15612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15613 0 1 2 100 hg38.150200.bed.split15613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15614 0 1 2 100 hg38.150200.bed.split15614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15615 0 1 2 100 hg38.150200.bed.split15615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15616 0 1 2 100 hg38.150200.bed.split15616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15617 0 1 2 100 hg38.150200.bed.split15617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15618 0 1 2 100 hg38.150200.bed.split15618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15619 0 1 2 100 hg38.150200.bed.split15619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1562 0 1 2 100 hg38.150200.bed.split1562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15620 0 1 2 100 hg38.150200.bed.split15620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15621 0 1 2 100 hg38.150200.bed.split15621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15622 0 1 2 100 hg38.150200.bed.split15622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15623 0 1 2 100 hg38.150200.bed.split15623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15624 0 1 2 100 hg38.150200.bed.split15624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15625 0 1 2 100 hg38.150200.bed.split15625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15626 0 1 2 100 hg38.150200.bed.split15626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15627 0 1 2 100 hg38.150200.bed.split15627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15628 0 1 2 100 hg38.150200.bed.split15628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15629 0 1 2 100 hg38.150200.bed.split15629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1563 0 1 2 100 hg38.150200.bed.split1563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15630 0 1 2 100 hg38.150200.bed.split15630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15631 0 1 2 100 hg38.150200.bed.split15631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15632 0 1 2 100 hg38.150200.bed.split15632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15633 0 1 2 100 hg38.150200.bed.split15633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15634 0 1 2 100 hg38.150200.bed.split15634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15635 0 1 2 100 hg38.150200.bed.split15635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15636 0 1 2 100 hg38.150200.bed.split15636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15637 0 1 2 100 hg38.150200.bed.split15637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15638 0 1 2 100 hg38.150200.bed.split15638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15639 0 1 2 100 hg38.150200.bed.split15639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1564 0 1 2 100 hg38.150200.bed.split1564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15640 0 1 2 100 hg38.150200.bed.split15640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15641 0 1 2 100 hg38.150200.bed.split15641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15642 0 1 2 100 hg38.150200.bed.split15642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15643 0 1 2 100 hg38.150200.bed.split15643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15644 0 1 2 100 hg38.150200.bed.split15644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15645 0 1 2 100 hg38.150200.bed.split15645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15646 0 1 2 100 hg38.150200.bed.split15646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15647 0 1 2 100 hg38.150200.bed.split15647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15648 0 1 2 100 hg38.150200.bed.split15648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15649 0 1 2 100 hg38.150200.bed.split15649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1565 0 1 2 100 hg38.150200.bed.split1565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15650 0 1 2 100 hg38.150200.bed.split15650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15651 0 1 2 100 hg38.150200.bed.split15651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15652 0 1 2 100 hg38.150200.bed.split15652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15653 0 1 2 100 hg38.150200.bed.split15653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15654 0 1 2 100 hg38.150200.bed.split15654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15655 0 1 2 100 hg38.150200.bed.split15655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15656 0 1 2 100 hg38.150200.bed.split15656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15657 0 1 2 100 hg38.150200.bed.split15657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15658 0 1 2 100 hg38.150200.bed.split15658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15659 0 1 2 100 hg38.150200.bed.split15659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1566 0 1 2 100 hg38.150200.bed.split1566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15660 0 1 2 100 hg38.150200.bed.split15660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15661 0 1 2 100 hg38.150200.bed.split15661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15662 0 1 2 100 hg38.150200.bed.split15662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15663 0 1 2 100 hg38.150200.bed.split15663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15664 0 1 2 100 hg38.150200.bed.split15664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15665 0 1 2 100 hg38.150200.bed.split15665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15666 0 1 2 100 hg38.150200.bed.split15666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15667 0 1 2 100 hg38.150200.bed.split15667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15668 0 1 2 100 hg38.150200.bed.split15668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15669 0 1 2 100 hg38.150200.bed.split15669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1567 0 1 2 100 hg38.150200.bed.split1567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15670 0 1 2 100 hg38.150200.bed.split15670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15671 0 1 2 100 hg38.150200.bed.split15671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15672 0 1 2 100 hg38.150200.bed.split15672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15673 0 1 2 100 hg38.150200.bed.split15673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15674 0 1 2 100 hg38.150200.bed.split15674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15675 0 1 2 100 hg38.150200.bed.split15675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15676 0 1 2 100 hg38.150200.bed.split15676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15677 0 1 2 100 hg38.150200.bed.split15677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15678 0 1 2 100 hg38.150200.bed.split15678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15679 0 1 2 100 hg38.150200.bed.split15679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1568 0 1 2 100 hg38.150200.bed.split1568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15680 0 1 2 100 hg38.150200.bed.split15680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15681 0 1 2 100 hg38.150200.bed.split15681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15682 0 1 2 100 hg38.150200.bed.split15682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15683 0 1 2 100 hg38.150200.bed.split15683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15684 0 1 2 100 hg38.150200.bed.split15684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15685 0 1 2 100 hg38.150200.bed.split15685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15686 0 1 2 100 hg38.150200.bed.split15686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15687 0 1 2 100 hg38.150200.bed.split15687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15688 0 1 2 100 hg38.150200.bed.split15688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15689 0 1 2 100 hg38.150200.bed.split15689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1569 0 1 2 100 hg38.150200.bed.split1569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15690 0 1 2 100 hg38.150200.bed.split15690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15691 0 1 2 100 hg38.150200.bed.split15691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15692 0 1 2 100 hg38.150200.bed.split15692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15693 0 1 2 100 hg38.150200.bed.split15693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15694 0 1 2 100 hg38.150200.bed.split15694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15695 0 1 2 100 hg38.150200.bed.split15695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15696 0 1 2 100 hg38.150200.bed.split15696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15697 0 1 2 100 hg38.150200.bed.split15697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15698 0 1 2 100 hg38.150200.bed.split15698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15699 0 1 2 100 hg38.150200.bed.split15699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split157 0 1 2 100 hg38.150200.bed.split157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1570 0 1 2 100 hg38.150200.bed.split1570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15700 0 1 2 100 hg38.150200.bed.split15700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15701 0 1 2 100 hg38.150200.bed.split15701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15702 0 1 2 100 hg38.150200.bed.split15702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15703 0 1 2 100 hg38.150200.bed.split15703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15704 0 1 2 100 hg38.150200.bed.split15704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15705 0 1 2 100 hg38.150200.bed.split15705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15706 0 1 2 100 hg38.150200.bed.split15706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15707 0 1 2 100 hg38.150200.bed.split15707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15708 0 1 2 100 hg38.150200.bed.split15708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15709 0 1 2 100 hg38.150200.bed.split15709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1571 0 1 2 100 hg38.150200.bed.split1571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15710 0 1 2 100 hg38.150200.bed.split15710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15711 0 1 2 100 hg38.150200.bed.split15711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15712 0 1 2 100 hg38.150200.bed.split15712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15713 0 1 2 100 hg38.150200.bed.split15713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15714 0 1 2 100 hg38.150200.bed.split15714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15715 0 1 2 100 hg38.150200.bed.split15715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15716 0 1 2 100 hg38.150200.bed.split15716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15717 0 1 2 100 hg38.150200.bed.split15717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15718 0 1 2 100 hg38.150200.bed.split15718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15719 0 1 2 100 hg38.150200.bed.split15719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1572 0 1 2 100 hg38.150200.bed.split1572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15720 0 1 2 100 hg38.150200.bed.split15720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15721 0 1 2 100 hg38.150200.bed.split15721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15722 0 1 2 100 hg38.150200.bed.split15722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15723 0 1 2 100 hg38.150200.bed.split15723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15724 0 1 2 100 hg38.150200.bed.split15724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15725 0 1 2 100 hg38.150200.bed.split15725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15726 0 1 2 100 hg38.150200.bed.split15726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15727 0 1 2 100 hg38.150200.bed.split15727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15728 0 1 2 100 hg38.150200.bed.split15728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15729 0 1 2 100 hg38.150200.bed.split15729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1573 0 1 2 100 hg38.150200.bed.split1573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15730 0 1 2 100 hg38.150200.bed.split15730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15731 0 1 2 100 hg38.150200.bed.split15731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15732 0 1 2 100 hg38.150200.bed.split15732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15733 0 1 2 100 hg38.150200.bed.split15733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15734 0 1 2 100 hg38.150200.bed.split15734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15735 0 1 2 100 hg38.150200.bed.split15735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15736 0 1 2 100 hg38.150200.bed.split15736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15737 0 1 2 100 hg38.150200.bed.split15737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15738 0 1 2 100 hg38.150200.bed.split15738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15739 0 1 2 100 hg38.150200.bed.split15739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1574 0 1 2 100 hg38.150200.bed.split1574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15740 0 1 2 100 hg38.150200.bed.split15740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15741 0 1 2 100 hg38.150200.bed.split15741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15742 0 1 2 100 hg38.150200.bed.split15742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15743 0 1 2 100 hg38.150200.bed.split15743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15744 0 1 2 100 hg38.150200.bed.split15744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15745 0 1 2 100 hg38.150200.bed.split15745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15746 0 1 2 100 hg38.150200.bed.split15746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15747 0 1 2 100 hg38.150200.bed.split15747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15748 0 1 2 100 hg38.150200.bed.split15748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15749 0 1 2 100 hg38.150200.bed.split15749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1575 0 1 2 100 hg38.150200.bed.split1575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15750 0 1 2 100 hg38.150200.bed.split15750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15751 0 1 2 100 hg38.150200.bed.split15751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15752 0 1 2 100 hg38.150200.bed.split15752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15753 0 1 2 100 hg38.150200.bed.split15753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15754 0 1 2 100 hg38.150200.bed.split15754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15755 0 1 2 100 hg38.150200.bed.split15755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15756 0 1 2 100 hg38.150200.bed.split15756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15757 0 1 2 100 hg38.150200.bed.split15757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15758 0 1 2 100 hg38.150200.bed.split15758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15759 0 1 2 100 hg38.150200.bed.split15759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1576 0 1 2 100 hg38.150200.bed.split1576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15760 0 1 2 100 hg38.150200.bed.split15760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15761 0 1 2 100 hg38.150200.bed.split15761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15762 0 1 2 100 hg38.150200.bed.split15762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15763 0 1 2 100 hg38.150200.bed.split15763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15764 0 1 2 100 hg38.150200.bed.split15764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15765 0 1 2 100 hg38.150200.bed.split15765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15766 0 1 2 100 hg38.150200.bed.split15766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15767 0 1 2 100 hg38.150200.bed.split15767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15768 0 1 2 100 hg38.150200.bed.split15768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15769 0 1 2 100 hg38.150200.bed.split15769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1577 0 1 2 100 hg38.150200.bed.split1577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15770 0 1 2 100 hg38.150200.bed.split15770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15771 0 1 2 100 hg38.150200.bed.split15771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15772 0 1 2 100 hg38.150200.bed.split15772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15773 0 1 2 100 hg38.150200.bed.split15773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15774 0 1 2 100 hg38.150200.bed.split15774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15775 0 1 2 100 hg38.150200.bed.split15775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15776 0 1 2 100 hg38.150200.bed.split15776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15777 0 1 2 100 hg38.150200.bed.split15777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15778 0 1 2 100 hg38.150200.bed.split15778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15779 0 1 2 100 hg38.150200.bed.split15779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1578 0 1 2 100 hg38.150200.bed.split1578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15780 0 1 2 100 hg38.150200.bed.split15780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15781 0 1 2 100 hg38.150200.bed.split15781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15782 0 1 2 100 hg38.150200.bed.split15782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15783 0 1 2 100 hg38.150200.bed.split15783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15784 0 1 2 100 hg38.150200.bed.split15784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15785 0 1 2 100 hg38.150200.bed.split15785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15786 0 1 2 100 hg38.150200.bed.split15786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15787 0 1 2 100 hg38.150200.bed.split15787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15788 0 1 2 100 hg38.150200.bed.split15788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15789 0 1 2 100 hg38.150200.bed.split15789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1579 0 1 2 100 hg38.150200.bed.split1579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15790 0 1 2 100 hg38.150200.bed.split15790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15791 0 1 2 100 hg38.150200.bed.split15791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15792 0 1 2 100 hg38.150200.bed.split15792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15793 0 1 2 100 hg38.150200.bed.split15793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15794 0 1 2 100 hg38.150200.bed.split15794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15795 0 1 2 100 hg38.150200.bed.split15795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15796 0 1 2 100 hg38.150200.bed.split15796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15797 0 1 2 100 hg38.150200.bed.split15797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15798 0 1 2 100 hg38.150200.bed.split15798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15799 0 1 2 100 hg38.150200.bed.split15799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split158 0 1 2 100 hg38.150200.bed.split158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1580 0 1 2 100 hg38.150200.bed.split1580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15800 0 1 2 100 hg38.150200.bed.split15800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15801 0 1 2 100 hg38.150200.bed.split15801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15802 0 1 2 100 hg38.150200.bed.split15802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15803 0 1 2 100 hg38.150200.bed.split15803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15804 0 1 2 100 hg38.150200.bed.split15804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15805 0 1 2 100 hg38.150200.bed.split15805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15806 0 1 2 100 hg38.150200.bed.split15806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15807 0 1 2 100 hg38.150200.bed.split15807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15808 0 1 2 100 hg38.150200.bed.split15808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15809 0 1 2 100 hg38.150200.bed.split15809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1581 0 1 2 100 hg38.150200.bed.split1581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15810 0 1 2 100 hg38.150200.bed.split15810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15811 0 1 2 100 hg38.150200.bed.split15811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15812 0 1 2 100 hg38.150200.bed.split15812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15813 0 1 2 100 hg38.150200.bed.split15813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15814 0 1 2 100 hg38.150200.bed.split15814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15815 0 1 2 100 hg38.150200.bed.split15815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15816 0 1 2 100 hg38.150200.bed.split15816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15817 0 1 2 100 hg38.150200.bed.split15817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15818 0 1 2 100 hg38.150200.bed.split15818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15819 0 1 2 100 hg38.150200.bed.split15819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1582 0 1 2 100 hg38.150200.bed.split1582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15820 0 1 2 100 hg38.150200.bed.split15820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15821 0 1 2 100 hg38.150200.bed.split15821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15822 0 1 2 100 hg38.150200.bed.split15822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15823 0 1 2 100 hg38.150200.bed.split15823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15824 0 1 2 100 hg38.150200.bed.split15824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15825 0 1 2 100 hg38.150200.bed.split15825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15826 0 1 2 100 hg38.150200.bed.split15826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15827 0 1 2 100 hg38.150200.bed.split15827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15828 0 1 2 100 hg38.150200.bed.split15828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15829 0 1 2 100 hg38.150200.bed.split15829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1583 0 1 2 100 hg38.150200.bed.split1583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15830 0 1 2 100 hg38.150200.bed.split15830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15831 0 1 2 100 hg38.150200.bed.split15831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15832 0 1 2 100 hg38.150200.bed.split15832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15833 0 1 2 100 hg38.150200.bed.split15833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15834 0 1 2 100 hg38.150200.bed.split15834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15835 0 1 2 100 hg38.150200.bed.split15835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15836 0 1 2 100 hg38.150200.bed.split15836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15837 0 1 2 100 hg38.150200.bed.split15837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15838 0 1 2 100 hg38.150200.bed.split15838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15839 0 1 2 100 hg38.150200.bed.split15839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1584 0 1 2 100 hg38.150200.bed.split1584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15840 0 1 2 100 hg38.150200.bed.split15840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15841 0 1 2 100 hg38.150200.bed.split15841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15842 0 1 2 100 hg38.150200.bed.split15842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15843 0 1 2 100 hg38.150200.bed.split15843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15844 0 1 2 100 hg38.150200.bed.split15844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15845 0 1 2 100 hg38.150200.bed.split15845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15846 0 1 2 100 hg38.150200.bed.split15846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15847 0 1 2 100 hg38.150200.bed.split15847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15848 0 1 2 100 hg38.150200.bed.split15848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15849 0 1 2 100 hg38.150200.bed.split15849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1585 0 1 2 100 hg38.150200.bed.split1585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15850 0 1 2 100 hg38.150200.bed.split15850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15851 0 1 2 100 hg38.150200.bed.split15851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15852 0 1 2 100 hg38.150200.bed.split15852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15853 0 1 2 100 hg38.150200.bed.split15853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15854 0 1 2 100 hg38.150200.bed.split15854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15855 0 1 2 100 hg38.150200.bed.split15855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15856 0 1 2 100 hg38.150200.bed.split15856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15857 0 1 2 100 hg38.150200.bed.split15857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15858 0 1 2 100 hg38.150200.bed.split15858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15859 0 1 2 100 hg38.150200.bed.split15859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1586 0 1 2 100 hg38.150200.bed.split1586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15860 0 1 2 100 hg38.150200.bed.split15860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15861 0 1 2 100 hg38.150200.bed.split15861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15862 0 1 2 100 hg38.150200.bed.split15862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15863 0 1 2 100 hg38.150200.bed.split15863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15864 0 1 2 100 hg38.150200.bed.split15864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15865 0 1 2 100 hg38.150200.bed.split15865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15866 0 1 2 100 hg38.150200.bed.split15866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15867 0 1 2 100 hg38.150200.bed.split15867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15868 0 1 2 100 hg38.150200.bed.split15868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15869 0 1 2 100 hg38.150200.bed.split15869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1587 0 1 2 100 hg38.150200.bed.split1587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15870 0 1 2 100 hg38.150200.bed.split15870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15871 0 1 2 100 hg38.150200.bed.split15871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15872 0 1 2 100 hg38.150200.bed.split15872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15873 0 1 2 100 hg38.150200.bed.split15873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15874 0 1 2 100 hg38.150200.bed.split15874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15875 0 1 2 100 hg38.150200.bed.split15875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15876 0 1 2 100 hg38.150200.bed.split15876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15877 0 1 2 100 hg38.150200.bed.split15877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15878 0 1 2 100 hg38.150200.bed.split15878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15879 0 1 2 100 hg38.150200.bed.split15879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1588 0 1 2 100 hg38.150200.bed.split1588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15880 0 1 2 100 hg38.150200.bed.split15880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15881 0 1 2 100 hg38.150200.bed.split15881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15882 0 1 2 100 hg38.150200.bed.split15882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15883 0 1 2 100 hg38.150200.bed.split15883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15884 0 1 2 100 hg38.150200.bed.split15884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15885 0 1 2 100 hg38.150200.bed.split15885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15886 0 1 2 100 hg38.150200.bed.split15886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15887 0 1 2 100 hg38.150200.bed.split15887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15888 0 1 2 100 hg38.150200.bed.split15888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15889 0 1 2 100 hg38.150200.bed.split15889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1589 0 1 2 100 hg38.150200.bed.split1589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15890 0 1 2 100 hg38.150200.bed.split15890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15891 0 1 2 100 hg38.150200.bed.split15891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15892 0 1 2 100 hg38.150200.bed.split15892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15893 0 1 2 100 hg38.150200.bed.split15893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15894 0 1 2 100 hg38.150200.bed.split15894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15895 0 1 2 100 hg38.150200.bed.split15895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15896 0 1 2 100 hg38.150200.bed.split15896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15897 0 1 2 100 hg38.150200.bed.split15897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15898 0 1 2 100 hg38.150200.bed.split15898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15899 0 1 2 100 hg38.150200.bed.split15899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split159 0 1 2 100 hg38.150200.bed.split159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1590 0 1 2 100 hg38.150200.bed.split1590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15900 0 1 2 100 hg38.150200.bed.split15900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15901 0 1 2 100 hg38.150200.bed.split15901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15902 0 1 2 100 hg38.150200.bed.split15902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15903 0 1 2 100 hg38.150200.bed.split15903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15904 0 1 2 100 hg38.150200.bed.split15904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15905 0 1 2 100 hg38.150200.bed.split15905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15906 0 1 2 100 hg38.150200.bed.split15906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15907 0 1 2 100 hg38.150200.bed.split15907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15908 0 1 2 100 hg38.150200.bed.split15908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15909 0 1 2 100 hg38.150200.bed.split15909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1591 0 1 2 100 hg38.150200.bed.split1591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15910 0 1 2 100 hg38.150200.bed.split15910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15911 0 1 2 100 hg38.150200.bed.split15911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15912 0 1 2 100 hg38.150200.bed.split15912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15913 0 1 2 100 hg38.150200.bed.split15913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15914 0 1 2 100 hg38.150200.bed.split15914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15915 0 1 2 100 hg38.150200.bed.split15915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15916 0 1 2 100 hg38.150200.bed.split15916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15917 0 1 2 100 hg38.150200.bed.split15917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15918 0 1 2 100 hg38.150200.bed.split15918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15919 0 1 2 100 hg38.150200.bed.split15919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1592 0 1 2 100 hg38.150200.bed.split1592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15920 0 1 2 100 hg38.150200.bed.split15920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15921 0 1 2 100 hg38.150200.bed.split15921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15922 0 1 2 100 hg38.150200.bed.split15922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15923 0 1 2 100 hg38.150200.bed.split15923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15924 0 1 2 100 hg38.150200.bed.split15924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15925 0 1 2 100 hg38.150200.bed.split15925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15926 0 1 2 100 hg38.150200.bed.split15926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15927 0 1 2 100 hg38.150200.bed.split15927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15928 0 1 2 100 hg38.150200.bed.split15928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15929 0 1 2 100 hg38.150200.bed.split15929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1593 0 1 2 100 hg38.150200.bed.split1593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15930 0 1 2 100 hg38.150200.bed.split15930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15931 0 1 2 100 hg38.150200.bed.split15931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15932 0 1 2 100 hg38.150200.bed.split15932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15933 0 1 2 100 hg38.150200.bed.split15933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15934 0 1 2 100 hg38.150200.bed.split15934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15935 0 1 2 100 hg38.150200.bed.split15935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15936 0 1 2 100 hg38.150200.bed.split15936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15937 0 1 2 100 hg38.150200.bed.split15937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15938 0 1 2 100 hg38.150200.bed.split15938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15939 0 1 2 100 hg38.150200.bed.split15939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1594 0 1 2 100 hg38.150200.bed.split1594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15940 0 1 2 100 hg38.150200.bed.split15940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15941 0 1 2 100 hg38.150200.bed.split15941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15942 0 1 2 100 hg38.150200.bed.split15942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15943 0 1 2 100 hg38.150200.bed.split15943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15944 0 1 2 100 hg38.150200.bed.split15944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15945 0 1 2 100 hg38.150200.bed.split15945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15946 0 1 2 100 hg38.150200.bed.split15946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15947 0 1 2 100 hg38.150200.bed.split15947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15948 0 1 2 100 hg38.150200.bed.split15948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15949 0 1 2 100 hg38.150200.bed.split15949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1595 0 1 2 100 hg38.150200.bed.split1595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15950 0 1 2 100 hg38.150200.bed.split15950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15951 0 1 2 100 hg38.150200.bed.split15951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15952 0 1 2 100 hg38.150200.bed.split15952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15953 0 1 2 100 hg38.150200.bed.split15953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15954 0 1 2 100 hg38.150200.bed.split15954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15955 0 1 2 100 hg38.150200.bed.split15955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15956 0 1 2 100 hg38.150200.bed.split15956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15957 0 1 2 100 hg38.150200.bed.split15957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15958 0 1 2 100 hg38.150200.bed.split15958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15959 0 1 2 100 hg38.150200.bed.split15959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1596 0 1 2 100 hg38.150200.bed.split1596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15960 0 1 2 100 hg38.150200.bed.split15960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15961 0 1 2 100 hg38.150200.bed.split15961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15962 0 1 2 100 hg38.150200.bed.split15962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15963 0 1 2 100 hg38.150200.bed.split15963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15964 0 1 2 100 hg38.150200.bed.split15964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15965 0 1 2 100 hg38.150200.bed.split15965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15966 0 1 2 100 hg38.150200.bed.split15966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15967 0 1 2 100 hg38.150200.bed.split15967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15968 0 1 2 100 hg38.150200.bed.split15968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15969 0 1 2 100 hg38.150200.bed.split15969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1597 0 1 2 100 hg38.150200.bed.split1597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15970 0 1 2 100 hg38.150200.bed.split15970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15971 0 1 2 100 hg38.150200.bed.split15971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15972 0 1 2 100 hg38.150200.bed.split15972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15973 0 1 2 100 hg38.150200.bed.split15973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15974 0 1 2 100 hg38.150200.bed.split15974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15975 0 1 2 100 hg38.150200.bed.split15975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15976 0 1 2 100 hg38.150200.bed.split15976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15977 0 1 2 100 hg38.150200.bed.split15977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15978 0 1 2 100 hg38.150200.bed.split15978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15979 0 1 2 100 hg38.150200.bed.split15979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1598 0 1 2 100 hg38.150200.bed.split1598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15980 0 1 2 100 hg38.150200.bed.split15980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15981 0 1 2 100 hg38.150200.bed.split15981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15982 0 1 2 100 hg38.150200.bed.split15982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15983 0 1 2 100 hg38.150200.bed.split15983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15984 0 1 2 100 hg38.150200.bed.split15984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15985 0 1 2 100 hg38.150200.bed.split15985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15986 0 1 2 100 hg38.150200.bed.split15986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15987 0 1 2 100 hg38.150200.bed.split15987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15988 0 1 2 100 hg38.150200.bed.split15988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15989 0 1 2 100 hg38.150200.bed.split15989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1599 0 1 2 100 hg38.150200.bed.split1599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15990 0 1 2 100 hg38.150200.bed.split15990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15991 0 1 2 100 hg38.150200.bed.split15991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15992 0 1 2 100 hg38.150200.bed.split15992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15993 0 1 2 100 hg38.150200.bed.split15993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15994 0 1 2 100 hg38.150200.bed.split15994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15995 0 1 2 100 hg38.150200.bed.split15995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15996 0 1 2 100 hg38.150200.bed.split15996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15997 0 1 2 100 hg38.150200.bed.split15997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15998 0 1 2 100 hg38.150200.bed.split15998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split15999 0 1 2 100 hg38.150200.bed.split15999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16 0 1 2 100 hg38.150200.bed.split16.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split160 0 1 2 100 hg38.150200.bed.split160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1600 0 1 2 100 hg38.150200.bed.split1600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16000 0 1 2 100 hg38.150200.bed.split16000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16001 0 1 2 100 hg38.150200.bed.split16001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16002 0 1 2 100 hg38.150200.bed.split16002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16003 0 1 2 100 hg38.150200.bed.split16003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16004 0 1 2 100 hg38.150200.bed.split16004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16005 0 1 2 100 hg38.150200.bed.split16005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16006 0 1 2 100 hg38.150200.bed.split16006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16007 0 1 2 100 hg38.150200.bed.split16007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16008 0 1 2 100 hg38.150200.bed.split16008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16009 0 1 2 100 hg38.150200.bed.split16009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1601 0 1 2 100 hg38.150200.bed.split1601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16010 0 1 2 100 hg38.150200.bed.split16010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16011 0 1 2 100 hg38.150200.bed.split16011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16012 0 1 2 100 hg38.150200.bed.split16012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16013 0 1 2 100 hg38.150200.bed.split16013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16014 0 1 2 100 hg38.150200.bed.split16014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16015 0 1 2 100 hg38.150200.bed.split16015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16016 0 1 2 100 hg38.150200.bed.split16016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16017 0 1 2 100 hg38.150200.bed.split16017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16018 0 1 2 100 hg38.150200.bed.split16018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16019 0 1 2 100 hg38.150200.bed.split16019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1602 0 1 2 100 hg38.150200.bed.split1602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16020 0 1 2 100 hg38.150200.bed.split16020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16021 0 1 2 100 hg38.150200.bed.split16021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16022 0 1 2 100 hg38.150200.bed.split16022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16023 0 1 2 100 hg38.150200.bed.split16023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16024 0 1 2 100 hg38.150200.bed.split16024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16025 0 1 2 100 hg38.150200.bed.split16025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16026 0 1 2 100 hg38.150200.bed.split16026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16027 0 1 2 100 hg38.150200.bed.split16027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16028 0 1 2 100 hg38.150200.bed.split16028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16029 0 1 2 100 hg38.150200.bed.split16029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1603 0 1 2 100 hg38.150200.bed.split1603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16030 0 1 2 100 hg38.150200.bed.split16030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16031 0 1 2 100 hg38.150200.bed.split16031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16032 0 1 2 100 hg38.150200.bed.split16032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16033 0 1 2 100 hg38.150200.bed.split16033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16034 0 1 2 100 hg38.150200.bed.split16034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16035 0 1 2 100 hg38.150200.bed.split16035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16036 0 1 2 100 hg38.150200.bed.split16036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16037 0 1 2 100 hg38.150200.bed.split16037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16038 0 1 2 100 hg38.150200.bed.split16038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16039 0 1 2 100 hg38.150200.bed.split16039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1604 0 1 2 100 hg38.150200.bed.split1604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16040 0 1 2 100 hg38.150200.bed.split16040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16041 0 1 2 100 hg38.150200.bed.split16041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16042 0 1 2 100 hg38.150200.bed.split16042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16043 0 1 2 100 hg38.150200.bed.split16043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16044 0 1 2 100 hg38.150200.bed.split16044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16045 0 1 2 100 hg38.150200.bed.split16045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16046 0 1 2 100 hg38.150200.bed.split16046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16047 0 1 2 100 hg38.150200.bed.split16047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16048 0 1 2 100 hg38.150200.bed.split16048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16049 0 1 2 100 hg38.150200.bed.split16049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1605 0 1 2 100 hg38.150200.bed.split1605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16050 0 1 2 100 hg38.150200.bed.split16050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16051 0 1 2 100 hg38.150200.bed.split16051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16052 0 1 2 100 hg38.150200.bed.split16052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16053 0 1 2 100 hg38.150200.bed.split16053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16054 0 1 2 100 hg38.150200.bed.split16054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16055 0 1 2 100 hg38.150200.bed.split16055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16056 0 1 2 100 hg38.150200.bed.split16056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16057 0 1 2 100 hg38.150200.bed.split16057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16058 0 1 2 100 hg38.150200.bed.split16058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16059 0 1 2 100 hg38.150200.bed.split16059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1606 0 1 2 100 hg38.150200.bed.split1606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16060 0 1 2 100 hg38.150200.bed.split16060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16061 0 1 2 100 hg38.150200.bed.split16061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16062 0 1 2 100 hg38.150200.bed.split16062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16063 0 1 2 100 hg38.150200.bed.split16063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16064 0 1 2 100 hg38.150200.bed.split16064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16065 0 1 2 100 hg38.150200.bed.split16065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16066 0 1 2 100 hg38.150200.bed.split16066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16067 0 1 2 100 hg38.150200.bed.split16067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16068 0 1 2 100 hg38.150200.bed.split16068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16069 0 1 2 100 hg38.150200.bed.split16069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1607 0 1 2 100 hg38.150200.bed.split1607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16070 0 1 2 100 hg38.150200.bed.split16070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16071 0 1 2 100 hg38.150200.bed.split16071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16072 0 1 2 100 hg38.150200.bed.split16072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16073 0 1 2 100 hg38.150200.bed.split16073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16074 0 1 2 100 hg38.150200.bed.split16074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16075 0 1 2 100 hg38.150200.bed.split16075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16076 0 1 2 100 hg38.150200.bed.split16076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16077 0 1 2 100 hg38.150200.bed.split16077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16078 0 1 2 100 hg38.150200.bed.split16078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16079 0 1 2 100 hg38.150200.bed.split16079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1608 0 1 2 100 hg38.150200.bed.split1608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16080 0 1 2 100 hg38.150200.bed.split16080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16081 0 1 2 100 hg38.150200.bed.split16081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16082 0 1 2 100 hg38.150200.bed.split16082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16083 0 1 2 100 hg38.150200.bed.split16083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16084 0 1 2 100 hg38.150200.bed.split16084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16085 0 1 2 100 hg38.150200.bed.split16085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16086 0 1 2 100 hg38.150200.bed.split16086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16087 0 1 2 100 hg38.150200.bed.split16087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16088 0 1 2 100 hg38.150200.bed.split16088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16089 0 1 2 100 hg38.150200.bed.split16089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1609 0 1 2 100 hg38.150200.bed.split1609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16090 0 1 2 100 hg38.150200.bed.split16090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16091 0 1 2 100 hg38.150200.bed.split16091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16092 0 1 2 100 hg38.150200.bed.split16092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16093 0 1 2 100 hg38.150200.bed.split16093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16094 0 1 2 100 hg38.150200.bed.split16094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16095 0 1 2 100 hg38.150200.bed.split16095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16096 0 1 2 100 hg38.150200.bed.split16096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16097 0 1 2 100 hg38.150200.bed.split16097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16098 0 1 2 100 hg38.150200.bed.split16098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16099 0 1 2 100 hg38.150200.bed.split16099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split161 0 1 2 100 hg38.150200.bed.split161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1610 0 1 2 100 hg38.150200.bed.split1610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16100 0 1 2 100 hg38.150200.bed.split16100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16101 0 1 2 100 hg38.150200.bed.split16101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16102 0 1 2 100 hg38.150200.bed.split16102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16103 0 1 2 100 hg38.150200.bed.split16103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16104 0 1 2 100 hg38.150200.bed.split16104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16105 0 1 2 100 hg38.150200.bed.split16105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16106 0 1 2 100 hg38.150200.bed.split16106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16107 0 1 2 100 hg38.150200.bed.split16107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16108 0 1 2 100 hg38.150200.bed.split16108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16109 0 1 2 100 hg38.150200.bed.split16109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1611 0 1 2 100 hg38.150200.bed.split1611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16110 0 1 2 100 hg38.150200.bed.split16110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16111 0 1 2 100 hg38.150200.bed.split16111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16112 0 1 2 100 hg38.150200.bed.split16112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16113 0 1 2 100 hg38.150200.bed.split16113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16114 0 1 2 100 hg38.150200.bed.split16114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16115 0 1 2 100 hg38.150200.bed.split16115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16116 0 1 2 100 hg38.150200.bed.split16116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16117 0 1 2 100 hg38.150200.bed.split16117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16118 0 1 2 100 hg38.150200.bed.split16118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16119 0 1 2 100 hg38.150200.bed.split16119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1612 0 1 2 100 hg38.150200.bed.split1612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16120 0 1 2 100 hg38.150200.bed.split16120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16121 0 1 2 100 hg38.150200.bed.split16121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16122 0 1 2 100 hg38.150200.bed.split16122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16123 0 1 2 100 hg38.150200.bed.split16123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16124 0 1 2 100 hg38.150200.bed.split16124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16125 0 1 2 100 hg38.150200.bed.split16125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16126 0 1 2 100 hg38.150200.bed.split16126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16127 0 1 2 100 hg38.150200.bed.split16127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16128 0 1 2 100 hg38.150200.bed.split16128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16129 0 1 2 100 hg38.150200.bed.split16129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1613 0 1 2 100 hg38.150200.bed.split1613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16130 0 1 2 100 hg38.150200.bed.split16130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16131 0 1 2 100 hg38.150200.bed.split16131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16132 0 1 2 100 hg38.150200.bed.split16132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16133 0 1 2 100 hg38.150200.bed.split16133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16134 0 1 2 100 hg38.150200.bed.split16134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16135 0 1 2 100 hg38.150200.bed.split16135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16136 0 1 2 100 hg38.150200.bed.split16136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16137 0 1 2 100 hg38.150200.bed.split16137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16138 0 1 2 100 hg38.150200.bed.split16138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16139 0 1 2 100 hg38.150200.bed.split16139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1614 0 1 2 100 hg38.150200.bed.split1614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16140 0 1 2 100 hg38.150200.bed.split16140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16141 0 1 2 100 hg38.150200.bed.split16141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16142 0 1 2 100 hg38.150200.bed.split16142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16143 0 1 2 100 hg38.150200.bed.split16143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16144 0 1 2 100 hg38.150200.bed.split16144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16145 0 1 2 100 hg38.150200.bed.split16145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16146 0 1 2 100 hg38.150200.bed.split16146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16147 0 1 2 100 hg38.150200.bed.split16147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16148 0 1 2 100 hg38.150200.bed.split16148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16149 0 1 2 100 hg38.150200.bed.split16149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1615 0 1 2 100 hg38.150200.bed.split1615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16150 0 1 2 100 hg38.150200.bed.split16150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16151 0 1 2 100 hg38.150200.bed.split16151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16152 0 1 2 100 hg38.150200.bed.split16152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16153 0 1 2 100 hg38.150200.bed.split16153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16154 0 1 2 100 hg38.150200.bed.split16154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16155 0 1 2 100 hg38.150200.bed.split16155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16156 0 1 2 100 hg38.150200.bed.split16156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16157 0 1 2 100 hg38.150200.bed.split16157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16158 0 1 2 100 hg38.150200.bed.split16158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16159 0 1 2 100 hg38.150200.bed.split16159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1616 0 1 2 100 hg38.150200.bed.split1616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16160 0 1 2 100 hg38.150200.bed.split16160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16161 0 1 2 100 hg38.150200.bed.split16161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16162 0 1 2 100 hg38.150200.bed.split16162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16163 0 1 2 100 hg38.150200.bed.split16163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16164 0 1 2 100 hg38.150200.bed.split16164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16165 0 1 2 100 hg38.150200.bed.split16165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16166 0 1 2 100 hg38.150200.bed.split16166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16167 0 1 2 100 hg38.150200.bed.split16167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16168 0 1 2 100 hg38.150200.bed.split16168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16169 0 1 2 100 hg38.150200.bed.split16169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1617 0 1 2 100 hg38.150200.bed.split1617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16170 0 1 2 100 hg38.150200.bed.split16170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16171 0 1 2 100 hg38.150200.bed.split16171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16172 0 1 2 100 hg38.150200.bed.split16172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16173 0 1 2 100 hg38.150200.bed.split16173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16174 0 1 2 100 hg38.150200.bed.split16174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16175 0 1 2 100 hg38.150200.bed.split16175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16176 0 1 2 100 hg38.150200.bed.split16176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16177 0 1 2 100 hg38.150200.bed.split16177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16178 0 1 2 100 hg38.150200.bed.split16178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16179 0 1 2 100 hg38.150200.bed.split16179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1618 0 1 2 100 hg38.150200.bed.split1618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16180 0 1 2 100 hg38.150200.bed.split16180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16181 0 1 2 100 hg38.150200.bed.split16181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16182 0 1 2 100 hg38.150200.bed.split16182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16183 0 1 2 100 hg38.150200.bed.split16183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16184 0 1 2 100 hg38.150200.bed.split16184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16185 0 1 2 100 hg38.150200.bed.split16185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16186 0 1 2 100 hg38.150200.bed.split16186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16187 0 1 2 100 hg38.150200.bed.split16187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16188 0 1 2 100 hg38.150200.bed.split16188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16189 0 1 2 100 hg38.150200.bed.split16189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1619 0 1 2 100 hg38.150200.bed.split1619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16190 0 1 2 100 hg38.150200.bed.split16190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16191 0 1 2 100 hg38.150200.bed.split16191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16192 0 1 2 100 hg38.150200.bed.split16192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16193 0 1 2 100 hg38.150200.bed.split16193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16194 0 1 2 100 hg38.150200.bed.split16194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16195 0 1 2 100 hg38.150200.bed.split16195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16196 0 1 2 100 hg38.150200.bed.split16196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16197 0 1 2 100 hg38.150200.bed.split16197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16198 0 1 2 100 hg38.150200.bed.split16198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16199 0 1 2 100 hg38.150200.bed.split16199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split162 0 1 2 100 hg38.150200.bed.split162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1620 0 1 2 100 hg38.150200.bed.split1620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16200 0 1 2 100 hg38.150200.bed.split16200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16201 0 1 2 100 hg38.150200.bed.split16201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16202 0 1 2 100 hg38.150200.bed.split16202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16203 0 1 2 100 hg38.150200.bed.split16203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16204 0 1 2 100 hg38.150200.bed.split16204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16205 0 1 2 100 hg38.150200.bed.split16205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16206 0 1 2 100 hg38.150200.bed.split16206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16207 0 1 2 100 hg38.150200.bed.split16207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16208 0 1 2 100 hg38.150200.bed.split16208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16209 0 1 2 100 hg38.150200.bed.split16209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1621 0 1 2 100 hg38.150200.bed.split1621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16210 0 1 2 100 hg38.150200.bed.split16210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16211 0 1 2 100 hg38.150200.bed.split16211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16212 0 1 2 100 hg38.150200.bed.split16212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16213 0 1 2 100 hg38.150200.bed.split16213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16214 0 1 2 100 hg38.150200.bed.split16214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16215 0 1 2 100 hg38.150200.bed.split16215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16216 0 1 2 100 hg38.150200.bed.split16216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16217 0 1 2 100 hg38.150200.bed.split16217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16218 0 1 2 100 hg38.150200.bed.split16218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16219 0 1 2 100 hg38.150200.bed.split16219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1622 0 1 2 100 hg38.150200.bed.split1622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16220 0 1 2 100 hg38.150200.bed.split16220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16221 0 1 2 100 hg38.150200.bed.split16221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16222 0 1 2 100 hg38.150200.bed.split16222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16223 0 1 2 100 hg38.150200.bed.split16223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16224 0 1 2 100 hg38.150200.bed.split16224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16225 0 1 2 100 hg38.150200.bed.split16225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16226 0 1 2 100 hg38.150200.bed.split16226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16227 0 1 2 100 hg38.150200.bed.split16227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16228 0 1 2 100 hg38.150200.bed.split16228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16229 0 1 2 100 hg38.150200.bed.split16229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1623 0 1 2 100 hg38.150200.bed.split1623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16230 0 1 2 100 hg38.150200.bed.split16230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16231 0 1 2 100 hg38.150200.bed.split16231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16232 0 1 2 100 hg38.150200.bed.split16232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16233 0 1 2 100 hg38.150200.bed.split16233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16234 0 1 2 100 hg38.150200.bed.split16234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16235 0 1 2 100 hg38.150200.bed.split16235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16236 0 1 2 100 hg38.150200.bed.split16236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16237 0 1 2 100 hg38.150200.bed.split16237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16238 0 1 2 100 hg38.150200.bed.split16238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16239 0 1 2 100 hg38.150200.bed.split16239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1624 0 1 2 100 hg38.150200.bed.split1624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16240 0 1 2 100 hg38.150200.bed.split16240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16241 0 1 2 100 hg38.150200.bed.split16241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16242 0 1 2 100 hg38.150200.bed.split16242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16243 0 1 2 100 hg38.150200.bed.split16243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16244 0 1 2 100 hg38.150200.bed.split16244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16245 0 1 2 100 hg38.150200.bed.split16245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16246 0 1 2 100 hg38.150200.bed.split16246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16247 0 1 2 100 hg38.150200.bed.split16247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16248 0 1 2 100 hg38.150200.bed.split16248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16249 0 1 2 100 hg38.150200.bed.split16249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1625 0 1 2 100 hg38.150200.bed.split1625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16250 0 1 2 100 hg38.150200.bed.split16250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16251 0 1 2 100 hg38.150200.bed.split16251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16252 0 1 2 100 hg38.150200.bed.split16252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16253 0 1 2 100 hg38.150200.bed.split16253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16254 0 1 2 100 hg38.150200.bed.split16254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16255 0 1 2 100 hg38.150200.bed.split16255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16256 0 1 2 100 hg38.150200.bed.split16256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16257 0 1 2 100 hg38.150200.bed.split16257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16258 0 1 2 100 hg38.150200.bed.split16258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16259 0 1 2 100 hg38.150200.bed.split16259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1626 0 1 2 100 hg38.150200.bed.split1626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16260 0 1 2 100 hg38.150200.bed.split16260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16261 0 1 2 100 hg38.150200.bed.split16261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16262 0 1 2 100 hg38.150200.bed.split16262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16263 0 1 2 100 hg38.150200.bed.split16263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16264 0 1 2 100 hg38.150200.bed.split16264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16265 0 1 2 100 hg38.150200.bed.split16265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16266 0 1 2 100 hg38.150200.bed.split16266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16267 0 1 2 100 hg38.150200.bed.split16267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16268 0 1 2 100 hg38.150200.bed.split16268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16269 0 1 2 100 hg38.150200.bed.split16269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1627 0 1 2 100 hg38.150200.bed.split1627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16270 0 1 2 100 hg38.150200.bed.split16270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16271 0 1 2 100 hg38.150200.bed.split16271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16272 0 1 2 100 hg38.150200.bed.split16272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16273 0 1 2 100 hg38.150200.bed.split16273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16274 0 1 2 100 hg38.150200.bed.split16274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16275 0 1 2 100 hg38.150200.bed.split16275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16276 0 1 2 100 hg38.150200.bed.split16276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16277 0 1 2 100 hg38.150200.bed.split16277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16278 0 1 2 100 hg38.150200.bed.split16278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16279 0 1 2 100 hg38.150200.bed.split16279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1628 0 1 2 100 hg38.150200.bed.split1628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16280 0 1 2 100 hg38.150200.bed.split16280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16281 0 1 2 100 hg38.150200.bed.split16281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16282 0 1 2 100 hg38.150200.bed.split16282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16283 0 1 2 100 hg38.150200.bed.split16283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16284 0 1 2 100 hg38.150200.bed.split16284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16285 0 1 2 100 hg38.150200.bed.split16285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16286 0 1 2 100 hg38.150200.bed.split16286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16287 0 1 2 100 hg38.150200.bed.split16287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16288 0 1 2 100 hg38.150200.bed.split16288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16289 0 1 2 100 hg38.150200.bed.split16289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1629 0 1 2 100 hg38.150200.bed.split1629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16290 0 1 2 100 hg38.150200.bed.split16290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16291 0 1 2 100 hg38.150200.bed.split16291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16292 0 1 2 100 hg38.150200.bed.split16292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16293 0 1 2 100 hg38.150200.bed.split16293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16294 0 1 2 100 hg38.150200.bed.split16294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16295 0 1 2 100 hg38.150200.bed.split16295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16296 0 1 2 100 hg38.150200.bed.split16296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16297 0 1 2 100 hg38.150200.bed.split16297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16298 0 1 2 100 hg38.150200.bed.split16298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16299 0 1 2 100 hg38.150200.bed.split16299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split163 0 1 2 100 hg38.150200.bed.split163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1630 0 1 2 100 hg38.150200.bed.split1630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16300 0 1 2 100 hg38.150200.bed.split16300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16301 0 1 2 100 hg38.150200.bed.split16301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16302 0 1 2 100 hg38.150200.bed.split16302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16303 0 1 2 100 hg38.150200.bed.split16303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16304 0 1 2 100 hg38.150200.bed.split16304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16305 0 1 2 100 hg38.150200.bed.split16305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16306 0 1 2 100 hg38.150200.bed.split16306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16307 0 1 2 100 hg38.150200.bed.split16307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16308 0 1 2 100 hg38.150200.bed.split16308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16309 0 1 2 100 hg38.150200.bed.split16309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1631 0 1 2 100 hg38.150200.bed.split1631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16310 0 1 2 100 hg38.150200.bed.split16310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16311 0 1 2 100 hg38.150200.bed.split16311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16312 0 1 2 100 hg38.150200.bed.split16312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16313 0 1 2 100 hg38.150200.bed.split16313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16314 0 1 2 100 hg38.150200.bed.split16314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16315 0 1 2 100 hg38.150200.bed.split16315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16316 0 1 2 100 hg38.150200.bed.split16316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16317 0 1 2 100 hg38.150200.bed.split16317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16318 0 1 2 100 hg38.150200.bed.split16318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16319 0 1 2 100 hg38.150200.bed.split16319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1632 0 1 2 100 hg38.150200.bed.split1632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16320 0 1 2 100 hg38.150200.bed.split16320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16321 0 1 2 100 hg38.150200.bed.split16321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16322 0 1 2 100 hg38.150200.bed.split16322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16323 0 1 2 100 hg38.150200.bed.split16323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16324 0 1 2 100 hg38.150200.bed.split16324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16325 0 1 2 100 hg38.150200.bed.split16325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16326 0 1 2 100 hg38.150200.bed.split16326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16327 0 1 2 100 hg38.150200.bed.split16327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16328 0 1 2 100 hg38.150200.bed.split16328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16329 0 1 2 100 hg38.150200.bed.split16329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1633 0 1 2 100 hg38.150200.bed.split1633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16330 0 1 2 100 hg38.150200.bed.split16330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16331 0 1 2 100 hg38.150200.bed.split16331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16332 0 1 2 100 hg38.150200.bed.split16332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16333 0 1 2 100 hg38.150200.bed.split16333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16334 0 1 2 100 hg38.150200.bed.split16334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16335 0 1 2 100 hg38.150200.bed.split16335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16336 0 1 2 100 hg38.150200.bed.split16336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16337 0 1 2 100 hg38.150200.bed.split16337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16338 0 1 2 100 hg38.150200.bed.split16338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16339 0 1 2 100 hg38.150200.bed.split16339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1634 0 1 2 100 hg38.150200.bed.split1634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16340 0 1 2 100 hg38.150200.bed.split16340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16341 0 1 2 100 hg38.150200.bed.split16341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16342 0 1 2 100 hg38.150200.bed.split16342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16343 0 1 2 100 hg38.150200.bed.split16343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16344 0 1 2 100 hg38.150200.bed.split16344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16345 0 1 2 100 hg38.150200.bed.split16345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16346 0 1 2 100 hg38.150200.bed.split16346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16347 0 1 2 100 hg38.150200.bed.split16347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16348 0 1 2 100 hg38.150200.bed.split16348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16349 0 1 2 100 hg38.150200.bed.split16349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1635 0 1 2 100 hg38.150200.bed.split1635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16350 0 1 2 100 hg38.150200.bed.split16350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16351 0 1 2 100 hg38.150200.bed.split16351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16352 0 1 2 100 hg38.150200.bed.split16352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16353 0 1 2 100 hg38.150200.bed.split16353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16354 0 1 2 100 hg38.150200.bed.split16354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16355 0 1 2 100 hg38.150200.bed.split16355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16356 0 1 2 100 hg38.150200.bed.split16356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16357 0 1 2 100 hg38.150200.bed.split16357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16358 0 1 2 100 hg38.150200.bed.split16358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16359 0 1 2 100 hg38.150200.bed.split16359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1636 0 1 2 100 hg38.150200.bed.split1636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16360 0 1 2 100 hg38.150200.bed.split16360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16361 0 1 2 100 hg38.150200.bed.split16361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16362 0 1 2 100 hg38.150200.bed.split16362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16363 0 1 2 100 hg38.150200.bed.split16363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16364 0 1 2 100 hg38.150200.bed.split16364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16365 0 1 2 100 hg38.150200.bed.split16365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16366 0 1 2 100 hg38.150200.bed.split16366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16367 0 1 2 100 hg38.150200.bed.split16367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16368 0 1 2 100 hg38.150200.bed.split16368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16369 0 1 2 100 hg38.150200.bed.split16369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1637 0 1 2 100 hg38.150200.bed.split1637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16370 0 1 2 100 hg38.150200.bed.split16370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16371 0 1 2 100 hg38.150200.bed.split16371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16372 0 1 2 100 hg38.150200.bed.split16372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16373 0 1 2 100 hg38.150200.bed.split16373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16374 0 1 2 100 hg38.150200.bed.split16374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16375 0 1 2 100 hg38.150200.bed.split16375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16376 0 1 2 100 hg38.150200.bed.split16376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16377 0 1 2 100 hg38.150200.bed.split16377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16378 0 1 2 100 hg38.150200.bed.split16378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16379 0 1 2 100 hg38.150200.bed.split16379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1638 0 1 2 100 hg38.150200.bed.split1638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16380 0 1 2 100 hg38.150200.bed.split16380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16381 0 1 2 100 hg38.150200.bed.split16381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16382 0 1 2 100 hg38.150200.bed.split16382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16383 0 1 2 100 hg38.150200.bed.split16383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16384 0 1 2 100 hg38.150200.bed.split16384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16385 0 1 2 100 hg38.150200.bed.split16385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16386 0 1 2 100 hg38.150200.bed.split16386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16387 0 1 2 100 hg38.150200.bed.split16387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16388 0 1 2 100 hg38.150200.bed.split16388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16389 0 1 2 100 hg38.150200.bed.split16389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1639 0 1 2 100 hg38.150200.bed.split1639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16390 0 1 2 100 hg38.150200.bed.split16390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16391 0 1 2 100 hg38.150200.bed.split16391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16392 0 1 2 100 hg38.150200.bed.split16392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16393 0 1 2 100 hg38.150200.bed.split16393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16394 0 1 2 100 hg38.150200.bed.split16394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16395 0 1 2 100 hg38.150200.bed.split16395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16396 0 1 2 100 hg38.150200.bed.split16396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16397 0 1 2 100 hg38.150200.bed.split16397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16398 0 1 2 100 hg38.150200.bed.split16398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16399 0 1 2 100 hg38.150200.bed.split16399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split164 0 1 2 100 hg38.150200.bed.split164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1640 0 1 2 100 hg38.150200.bed.split1640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16400 0 1 2 100 hg38.150200.bed.split16400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16401 0 1 2 100 hg38.150200.bed.split16401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16402 0 1 2 100 hg38.150200.bed.split16402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16403 0 1 2 100 hg38.150200.bed.split16403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16404 0 1 2 100 hg38.150200.bed.split16404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16405 0 1 2 100 hg38.150200.bed.split16405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16406 0 1 2 100 hg38.150200.bed.split16406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16407 0 1 2 100 hg38.150200.bed.split16407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16408 0 1 2 100 hg38.150200.bed.split16408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16409 0 1 2 100 hg38.150200.bed.split16409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1641 0 1 2 100 hg38.150200.bed.split1641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16410 0 1 2 100 hg38.150200.bed.split16410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16411 0 1 2 100 hg38.150200.bed.split16411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16412 0 1 2 100 hg38.150200.bed.split16412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16413 0 1 2 100 hg38.150200.bed.split16413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16414 0 1 2 100 hg38.150200.bed.split16414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16415 0 1 2 100 hg38.150200.bed.split16415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16416 0 1 2 100 hg38.150200.bed.split16416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16417 0 1 2 100 hg38.150200.bed.split16417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16418 0 1 2 100 hg38.150200.bed.split16418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16419 0 1 2 100 hg38.150200.bed.split16419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1642 0 1 2 100 hg38.150200.bed.split1642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16420 0 1 2 100 hg38.150200.bed.split16420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16421 0 1 2 100 hg38.150200.bed.split16421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16422 0 1 2 100 hg38.150200.bed.split16422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16423 0 1 2 100 hg38.150200.bed.split16423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16424 0 1 2 100 hg38.150200.bed.split16424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16425 0 1 2 100 hg38.150200.bed.split16425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16426 0 1 2 100 hg38.150200.bed.split16426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16427 0 1 2 100 hg38.150200.bed.split16427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16428 0 1 2 100 hg38.150200.bed.split16428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16429 0 1 2 100 hg38.150200.bed.split16429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1643 0 1 2 100 hg38.150200.bed.split1643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16430 0 1 2 100 hg38.150200.bed.split16430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16431 0 1 2 100 hg38.150200.bed.split16431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16432 0 1 2 100 hg38.150200.bed.split16432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16433 0 1 2 100 hg38.150200.bed.split16433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16434 0 1 2 100 hg38.150200.bed.split16434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16435 0 1 2 100 hg38.150200.bed.split16435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16436 0 1 2 100 hg38.150200.bed.split16436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16437 0 1 2 100 hg38.150200.bed.split16437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16438 0 1 2 100 hg38.150200.bed.split16438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16439 0 1 2 100 hg38.150200.bed.split16439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1644 0 1 2 100 hg38.150200.bed.split1644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16440 0 1 2 100 hg38.150200.bed.split16440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16441 0 1 2 100 hg38.150200.bed.split16441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16442 0 1 2 100 hg38.150200.bed.split16442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16443 0 1 2 100 hg38.150200.bed.split16443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16444 0 1 2 100 hg38.150200.bed.split16444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16445 0 1 2 100 hg38.150200.bed.split16445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16446 0 1 2 100 hg38.150200.bed.split16446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16447 0 1 2 100 hg38.150200.bed.split16447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16448 0 1 2 100 hg38.150200.bed.split16448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16449 0 1 2 100 hg38.150200.bed.split16449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1645 0 1 2 100 hg38.150200.bed.split1645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16450 0 1 2 100 hg38.150200.bed.split16450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16451 0 1 2 100 hg38.150200.bed.split16451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16452 0 1 2 100 hg38.150200.bed.split16452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16453 0 1 2 100 hg38.150200.bed.split16453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16454 0 1 2 100 hg38.150200.bed.split16454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16455 0 1 2 100 hg38.150200.bed.split16455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16456 0 1 2 100 hg38.150200.bed.split16456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16457 0 1 2 100 hg38.150200.bed.split16457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16458 0 1 2 100 hg38.150200.bed.split16458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16459 0 1 2 100 hg38.150200.bed.split16459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1646 0 1 2 100 hg38.150200.bed.split1646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16460 0 1 2 100 hg38.150200.bed.split16460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16461 0 1 2 100 hg38.150200.bed.split16461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16462 0 1 2 100 hg38.150200.bed.split16462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16463 0 1 2 100 hg38.150200.bed.split16463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16464 0 1 2 100 hg38.150200.bed.split16464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16465 0 1 2 100 hg38.150200.bed.split16465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16466 0 1 2 100 hg38.150200.bed.split16466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16467 0 1 2 100 hg38.150200.bed.split16467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16468 0 1 2 100 hg38.150200.bed.split16468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16469 0 1 2 100 hg38.150200.bed.split16469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1647 0 1 2 100 hg38.150200.bed.split1647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16470 0 1 2 100 hg38.150200.bed.split16470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16471 0 1 2 100 hg38.150200.bed.split16471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16472 0 1 2 100 hg38.150200.bed.split16472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16473 0 1 2 100 hg38.150200.bed.split16473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16474 0 1 2 100 hg38.150200.bed.split16474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16475 0 1 2 100 hg38.150200.bed.split16475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16476 0 1 2 100 hg38.150200.bed.split16476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16477 0 1 2 100 hg38.150200.bed.split16477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16478 0 1 2 100 hg38.150200.bed.split16478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16479 0 1 2 100 hg38.150200.bed.split16479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1648 0 1 2 100 hg38.150200.bed.split1648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16480 0 1 2 100 hg38.150200.bed.split16480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16481 0 1 2 100 hg38.150200.bed.split16481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16482 0 1 2 100 hg38.150200.bed.split16482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16483 0 1 2 100 hg38.150200.bed.split16483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16484 0 1 2 100 hg38.150200.bed.split16484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16485 0 1 2 100 hg38.150200.bed.split16485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16486 0 1 2 100 hg38.150200.bed.split16486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16487 0 1 2 100 hg38.150200.bed.split16487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16488 0 1 2 100 hg38.150200.bed.split16488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16489 0 1 2 100 hg38.150200.bed.split16489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1649 0 1 2 100 hg38.150200.bed.split1649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16490 0 1 2 100 hg38.150200.bed.split16490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16491 0 1 2 100 hg38.150200.bed.split16491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16492 0 1 2 100 hg38.150200.bed.split16492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16493 0 1 2 100 hg38.150200.bed.split16493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16494 0 1 2 100 hg38.150200.bed.split16494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16495 0 1 2 100 hg38.150200.bed.split16495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16496 0 1 2 100 hg38.150200.bed.split16496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16497 0 1 2 100 hg38.150200.bed.split16497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16498 0 1 2 100 hg38.150200.bed.split16498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16499 0 1 2 100 hg38.150200.bed.split16499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split165 0 1 2 100 hg38.150200.bed.split165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1650 0 1 2 100 hg38.150200.bed.split1650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16500 0 1 2 100 hg38.150200.bed.split16500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16501 0 1 2 100 hg38.150200.bed.split16501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16502 0 1 2 100 hg38.150200.bed.split16502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16503 0 1 2 100 hg38.150200.bed.split16503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16504 0 1 2 100 hg38.150200.bed.split16504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16505 0 1 2 100 hg38.150200.bed.split16505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16506 0 1 2 100 hg38.150200.bed.split16506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16507 0 1 2 100 hg38.150200.bed.split16507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16508 0 1 2 100 hg38.150200.bed.split16508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16509 0 1 2 100 hg38.150200.bed.split16509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1651 0 1 2 100 hg38.150200.bed.split1651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16510 0 1 2 100 hg38.150200.bed.split16510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16511 0 1 2 100 hg38.150200.bed.split16511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16512 0 1 2 100 hg38.150200.bed.split16512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16513 0 1 2 100 hg38.150200.bed.split16513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16514 0 1 2 100 hg38.150200.bed.split16514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16515 0 1 2 100 hg38.150200.bed.split16515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16516 0 1 2 100 hg38.150200.bed.split16516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16517 0 1 2 100 hg38.150200.bed.split16517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16518 0 1 2 100 hg38.150200.bed.split16518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16519 0 1 2 100 hg38.150200.bed.split16519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1652 0 1 2 100 hg38.150200.bed.split1652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16520 0 1 2 100 hg38.150200.bed.split16520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16521 0 1 2 100 hg38.150200.bed.split16521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16522 0 1 2 100 hg38.150200.bed.split16522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16523 0 1 2 100 hg38.150200.bed.split16523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16524 0 1 2 100 hg38.150200.bed.split16524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16525 0 1 2 100 hg38.150200.bed.split16525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16526 0 1 2 100 hg38.150200.bed.split16526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16527 0 1 2 100 hg38.150200.bed.split16527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16528 0 1 2 100 hg38.150200.bed.split16528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16529 0 1 2 100 hg38.150200.bed.split16529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1653 0 1 2 100 hg38.150200.bed.split1653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16530 0 1 2 100 hg38.150200.bed.split16530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16531 0 1 2 100 hg38.150200.bed.split16531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16532 0 1 2 100 hg38.150200.bed.split16532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16533 0 1 2 100 hg38.150200.bed.split16533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16534 0 1 2 100 hg38.150200.bed.split16534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16535 0 1 2 100 hg38.150200.bed.split16535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16536 0 1 2 100 hg38.150200.bed.split16536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16537 0 1 2 100 hg38.150200.bed.split16537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16538 0 1 2 100 hg38.150200.bed.split16538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16539 0 1 2 100 hg38.150200.bed.split16539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1654 0 1 2 100 hg38.150200.bed.split1654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16540 0 1 2 100 hg38.150200.bed.split16540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16541 0 1 2 100 hg38.150200.bed.split16541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16542 0 1 2 100 hg38.150200.bed.split16542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16543 0 1 2 100 hg38.150200.bed.split16543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16544 0 1 2 100 hg38.150200.bed.split16544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16545 0 1 2 100 hg38.150200.bed.split16545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16546 0 1 2 100 hg38.150200.bed.split16546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16547 0 1 2 100 hg38.150200.bed.split16547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16548 0 1 2 100 hg38.150200.bed.split16548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16549 0 1 2 100 hg38.150200.bed.split16549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1655 0 1 2 100 hg38.150200.bed.split1655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16550 0 1 2 100 hg38.150200.bed.split16550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16551 0 1 2 100 hg38.150200.bed.split16551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16552 0 1 2 100 hg38.150200.bed.split16552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16553 0 1 2 100 hg38.150200.bed.split16553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16554 0 1 2 100 hg38.150200.bed.split16554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16555 0 1 2 100 hg38.150200.bed.split16555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16556 0 1 2 100 hg38.150200.bed.split16556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16557 0 1 2 100 hg38.150200.bed.split16557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16558 0 1 2 100 hg38.150200.bed.split16558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16559 0 1 2 100 hg38.150200.bed.split16559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1656 0 1 2 100 hg38.150200.bed.split1656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16560 0 1 2 100 hg38.150200.bed.split16560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16561 0 1 2 100 hg38.150200.bed.split16561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16562 0 1 2 100 hg38.150200.bed.split16562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16563 0 1 2 100 hg38.150200.bed.split16563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16564 0 1 2 100 hg38.150200.bed.split16564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16565 0 1 2 100 hg38.150200.bed.split16565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16566 0 1 2 100 hg38.150200.bed.split16566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16567 0 1 2 100 hg38.150200.bed.split16567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16568 0 1 2 100 hg38.150200.bed.split16568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16569 0 1 2 100 hg38.150200.bed.split16569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1657 0 1 2 100 hg38.150200.bed.split1657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16570 0 1 2 100 hg38.150200.bed.split16570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16571 0 1 2 100 hg38.150200.bed.split16571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16572 0 1 2 100 hg38.150200.bed.split16572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16573 0 1 2 100 hg38.150200.bed.split16573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16574 0 1 2 100 hg38.150200.bed.split16574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16575 0 1 2 100 hg38.150200.bed.split16575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16576 0 1 2 100 hg38.150200.bed.split16576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16577 0 1 2 100 hg38.150200.bed.split16577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16578 0 1 2 100 hg38.150200.bed.split16578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16579 0 1 2 100 hg38.150200.bed.split16579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1658 0 1 2 100 hg38.150200.bed.split1658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16580 0 1 2 100 hg38.150200.bed.split16580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16581 0 1 2 100 hg38.150200.bed.split16581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16582 0 1 2 100 hg38.150200.bed.split16582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16583 0 1 2 100 hg38.150200.bed.split16583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16584 0 1 2 100 hg38.150200.bed.split16584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16585 0 1 2 100 hg38.150200.bed.split16585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16586 0 1 2 100 hg38.150200.bed.split16586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16587 0 1 2 100 hg38.150200.bed.split16587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16588 0 1 2 100 hg38.150200.bed.split16588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16589 0 1 2 100 hg38.150200.bed.split16589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1659 0 1 2 100 hg38.150200.bed.split1659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16590 0 1 2 100 hg38.150200.bed.split16590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16591 0 1 2 100 hg38.150200.bed.split16591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16592 0 1 2 100 hg38.150200.bed.split16592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16593 0 1 2 100 hg38.150200.bed.split16593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16594 0 1 2 100 hg38.150200.bed.split16594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16595 0 1 2 100 hg38.150200.bed.split16595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16596 0 1 2 100 hg38.150200.bed.split16596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16597 0 1 2 100 hg38.150200.bed.split16597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16598 0 1 2 100 hg38.150200.bed.split16598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16599 0 1 2 100 hg38.150200.bed.split16599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split166 0 1 2 100 hg38.150200.bed.split166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1660 0 1 2 100 hg38.150200.bed.split1660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16600 0 1 2 100 hg38.150200.bed.split16600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16601 0 1 2 100 hg38.150200.bed.split16601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16602 0 1 2 100 hg38.150200.bed.split16602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16603 0 1 2 100 hg38.150200.bed.split16603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16604 0 1 2 100 hg38.150200.bed.split16604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16605 0 1 2 100 hg38.150200.bed.split16605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16606 0 1 2 100 hg38.150200.bed.split16606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16607 0 1 2 100 hg38.150200.bed.split16607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16608 0 1 2 100 hg38.150200.bed.split16608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16609 0 1 2 100 hg38.150200.bed.split16609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1661 0 1 2 100 hg38.150200.bed.split1661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16610 0 1 2 100 hg38.150200.bed.split16610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16611 0 1 2 100 hg38.150200.bed.split16611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16612 0 1 2 100 hg38.150200.bed.split16612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16613 0 1 2 100 hg38.150200.bed.split16613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16614 0 1 2 100 hg38.150200.bed.split16614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16615 0 1 2 100 hg38.150200.bed.split16615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16616 0 1 2 100 hg38.150200.bed.split16616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16617 0 1 2 100 hg38.150200.bed.split16617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16618 0 1 2 100 hg38.150200.bed.split16618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16619 0 1 2 100 hg38.150200.bed.split16619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1662 0 1 2 100 hg38.150200.bed.split1662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16620 0 1 2 100 hg38.150200.bed.split16620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16621 0 1 2 100 hg38.150200.bed.split16621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16622 0 1 2 100 hg38.150200.bed.split16622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16623 0 1 2 100 hg38.150200.bed.split16623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16624 0 1 2 100 hg38.150200.bed.split16624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16625 0 1 2 100 hg38.150200.bed.split16625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16626 0 1 2 100 hg38.150200.bed.split16626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16627 0 1 2 100 hg38.150200.bed.split16627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16628 0 1 2 100 hg38.150200.bed.split16628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16629 0 1 2 100 hg38.150200.bed.split16629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1663 0 1 2 100 hg38.150200.bed.split1663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16630 0 1 2 100 hg38.150200.bed.split16630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16631 0 1 2 100 hg38.150200.bed.split16631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16632 0 1 2 100 hg38.150200.bed.split16632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16633 0 1 2 100 hg38.150200.bed.split16633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16634 0 1 2 100 hg38.150200.bed.split16634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16635 0 1 2 100 hg38.150200.bed.split16635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16636 0 1 2 100 hg38.150200.bed.split16636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16637 0 1 2 100 hg38.150200.bed.split16637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16638 0 1 2 100 hg38.150200.bed.split16638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16639 0 1 2 100 hg38.150200.bed.split16639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1664 0 1 2 100 hg38.150200.bed.split1664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16640 0 1 2 100 hg38.150200.bed.split16640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16641 0 1 2 100 hg38.150200.bed.split16641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16642 0 1 2 100 hg38.150200.bed.split16642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16643 0 1 2 100 hg38.150200.bed.split16643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16644 0 1 2 100 hg38.150200.bed.split16644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16645 0 1 2 100 hg38.150200.bed.split16645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16646 0 1 2 100 hg38.150200.bed.split16646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16647 0 1 2 100 hg38.150200.bed.split16647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16648 0 1 2 100 hg38.150200.bed.split16648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16649 0 1 2 100 hg38.150200.bed.split16649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1665 0 1 2 100 hg38.150200.bed.split1665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16650 0 1 2 100 hg38.150200.bed.split16650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16651 0 1 2 100 hg38.150200.bed.split16651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16652 0 1 2 100 hg38.150200.bed.split16652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16653 0 1 2 100 hg38.150200.bed.split16653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16654 0 1 2 100 hg38.150200.bed.split16654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16655 0 1 2 100 hg38.150200.bed.split16655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16656 0 1 2 100 hg38.150200.bed.split16656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16657 0 1 2 100 hg38.150200.bed.split16657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16658 0 1 2 100 hg38.150200.bed.split16658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16659 0 1 2 100 hg38.150200.bed.split16659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1666 0 1 2 100 hg38.150200.bed.split1666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16660 0 1 2 100 hg38.150200.bed.split16660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16661 0 1 2 100 hg38.150200.bed.split16661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16662 0 1 2 100 hg38.150200.bed.split16662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16663 0 1 2 100 hg38.150200.bed.split16663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16664 0 1 2 100 hg38.150200.bed.split16664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16665 0 1 2 100 hg38.150200.bed.split16665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16666 0 1 2 100 hg38.150200.bed.split16666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16667 0 1 2 100 hg38.150200.bed.split16667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16668 0 1 2 100 hg38.150200.bed.split16668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16669 0 1 2 100 hg38.150200.bed.split16669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1667 0 1 2 100 hg38.150200.bed.split1667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16670 0 1 2 100 hg38.150200.bed.split16670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16671 0 1 2 100 hg38.150200.bed.split16671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16672 0 1 2 100 hg38.150200.bed.split16672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16673 0 1 2 100 hg38.150200.bed.split16673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16674 0 1 2 100 hg38.150200.bed.split16674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16675 0 1 2 100 hg38.150200.bed.split16675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16676 0 1 2 100 hg38.150200.bed.split16676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16677 0 1 2 100 hg38.150200.bed.split16677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16678 0 1 2 100 hg38.150200.bed.split16678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16679 0 1 2 100 hg38.150200.bed.split16679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1668 0 1 2 100 hg38.150200.bed.split1668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16680 0 1 2 100 hg38.150200.bed.split16680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16681 0 1 2 100 hg38.150200.bed.split16681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16682 0 1 2 100 hg38.150200.bed.split16682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16683 0 1 2 100 hg38.150200.bed.split16683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16684 0 1 2 100 hg38.150200.bed.split16684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16685 0 1 2 100 hg38.150200.bed.split16685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16686 0 1 2 100 hg38.150200.bed.split16686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16687 0 1 2 100 hg38.150200.bed.split16687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16688 0 1 2 100 hg38.150200.bed.split16688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16689 0 1 2 100 hg38.150200.bed.split16689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1669 0 1 2 100 hg38.150200.bed.split1669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16690 0 1 2 100 hg38.150200.bed.split16690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16691 0 1 2 100 hg38.150200.bed.split16691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16692 0 1 2 100 hg38.150200.bed.split16692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16693 0 1 2 100 hg38.150200.bed.split16693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16694 0 1 2 100 hg38.150200.bed.split16694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16695 0 1 2 100 hg38.150200.bed.split16695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16696 0 1 2 100 hg38.150200.bed.split16696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16697 0 1 2 100 hg38.150200.bed.split16697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16698 0 1 2 100 hg38.150200.bed.split16698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16699 0 1 2 100 hg38.150200.bed.split16699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split167 0 1 2 100 hg38.150200.bed.split167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1670 0 1 2 100 hg38.150200.bed.split1670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16700 0 1 2 100 hg38.150200.bed.split16700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16701 0 1 2 100 hg38.150200.bed.split16701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16702 0 1 2 100 hg38.150200.bed.split16702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16703 0 1 2 100 hg38.150200.bed.split16703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16704 0 1 2 100 hg38.150200.bed.split16704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16705 0 1 2 100 hg38.150200.bed.split16705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16706 0 1 2 100 hg38.150200.bed.split16706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16707 0 1 2 100 hg38.150200.bed.split16707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16708 0 1 2 100 hg38.150200.bed.split16708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16709 0 1 2 100 hg38.150200.bed.split16709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1671 0 1 2 100 hg38.150200.bed.split1671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16710 0 1 2 100 hg38.150200.bed.split16710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16711 0 1 2 100 hg38.150200.bed.split16711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16712 0 1 2 100 hg38.150200.bed.split16712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16713 0 1 2 100 hg38.150200.bed.split16713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16714 0 1 2 100 hg38.150200.bed.split16714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16715 0 1 2 100 hg38.150200.bed.split16715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16716 0 1 2 100 hg38.150200.bed.split16716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16717 0 1 2 100 hg38.150200.bed.split16717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16718 0 1 2 100 hg38.150200.bed.split16718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16719 0 1 2 100 hg38.150200.bed.split16719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1672 0 1 2 100 hg38.150200.bed.split1672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16720 0 1 2 100 hg38.150200.bed.split16720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16721 0 1 2 100 hg38.150200.bed.split16721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16722 0 1 2 100 hg38.150200.bed.split16722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16723 0 1 2 100 hg38.150200.bed.split16723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16724 0 1 2 100 hg38.150200.bed.split16724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16725 0 1 2 100 hg38.150200.bed.split16725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16726 0 1 2 100 hg38.150200.bed.split16726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16727 0 1 2 100 hg38.150200.bed.split16727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16728 0 1 2 100 hg38.150200.bed.split16728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16729 0 1 2 100 hg38.150200.bed.split16729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1673 0 1 2 100 hg38.150200.bed.split1673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16730 0 1 2 100 hg38.150200.bed.split16730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16731 0 1 2 100 hg38.150200.bed.split16731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16732 0 1 2 100 hg38.150200.bed.split16732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16733 0 1 2 100 hg38.150200.bed.split16733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16734 0 1 2 100 hg38.150200.bed.split16734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16735 0 1 2 100 hg38.150200.bed.split16735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16736 0 1 2 100 hg38.150200.bed.split16736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16737 0 1 2 100 hg38.150200.bed.split16737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16738 0 1 2 100 hg38.150200.bed.split16738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16739 0 1 2 100 hg38.150200.bed.split16739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1674 0 1 2 100 hg38.150200.bed.split1674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16740 0 1 2 100 hg38.150200.bed.split16740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16741 0 1 2 100 hg38.150200.bed.split16741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16742 0 1 2 100 hg38.150200.bed.split16742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16743 0 1 2 100 hg38.150200.bed.split16743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16744 0 1 2 100 hg38.150200.bed.split16744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16745 0 1 2 100 hg38.150200.bed.split16745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16746 0 1 2 100 hg38.150200.bed.split16746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16747 0 1 2 100 hg38.150200.bed.split16747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16748 0 1 2 100 hg38.150200.bed.split16748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16749 0 1 2 100 hg38.150200.bed.split16749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1675 0 1 2 100 hg38.150200.bed.split1675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16750 0 1 2 100 hg38.150200.bed.split16750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16751 0 1 2 100 hg38.150200.bed.split16751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16752 0 1 2 100 hg38.150200.bed.split16752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16753 0 1 2 100 hg38.150200.bed.split16753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16754 0 1 2 100 hg38.150200.bed.split16754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16755 0 1 2 100 hg38.150200.bed.split16755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16756 0 1 2 100 hg38.150200.bed.split16756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16757 0 1 2 100 hg38.150200.bed.split16757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16758 0 1 2 100 hg38.150200.bed.split16758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16759 0 1 2 100 hg38.150200.bed.split16759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1676 0 1 2 100 hg38.150200.bed.split1676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16760 0 1 2 100 hg38.150200.bed.split16760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16761 0 1 2 100 hg38.150200.bed.split16761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16762 0 1 2 100 hg38.150200.bed.split16762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16763 0 1 2 100 hg38.150200.bed.split16763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16764 0 1 2 100 hg38.150200.bed.split16764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16765 0 1 2 100 hg38.150200.bed.split16765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16766 0 1 2 100 hg38.150200.bed.split16766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16767 0 1 2 100 hg38.150200.bed.split16767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16768 0 1 2 100 hg38.150200.bed.split16768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16769 0 1 2 100 hg38.150200.bed.split16769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1677 0 1 2 100 hg38.150200.bed.split1677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16770 0 1 2 100 hg38.150200.bed.split16770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16771 0 1 2 100 hg38.150200.bed.split16771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16772 0 1 2 100 hg38.150200.bed.split16772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16773 0 1 2 100 hg38.150200.bed.split16773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16774 0 1 2 100 hg38.150200.bed.split16774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16775 0 1 2 100 hg38.150200.bed.split16775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16776 0 1 2 100 hg38.150200.bed.split16776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16777 0 1 2 100 hg38.150200.bed.split16777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16778 0 1 2 100 hg38.150200.bed.split16778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16779 0 1 2 100 hg38.150200.bed.split16779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1678 0 1 2 100 hg38.150200.bed.split1678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16780 0 1 2 100 hg38.150200.bed.split16780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16781 0 1 2 100 hg38.150200.bed.split16781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16782 0 1 2 100 hg38.150200.bed.split16782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16783 0 1 2 100 hg38.150200.bed.split16783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16784 0 1 2 100 hg38.150200.bed.split16784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16785 0 1 2 100 hg38.150200.bed.split16785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16786 0 1 2 100 hg38.150200.bed.split16786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16787 0 1 2 100 hg38.150200.bed.split16787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16788 0 1 2 100 hg38.150200.bed.split16788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16789 0 1 2 100 hg38.150200.bed.split16789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1679 0 1 2 100 hg38.150200.bed.split1679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16790 0 1 2 100 hg38.150200.bed.split16790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16791 0 1 2 100 hg38.150200.bed.split16791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16792 0 1 2 100 hg38.150200.bed.split16792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16793 0 1 2 100 hg38.150200.bed.split16793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16794 0 1 2 100 hg38.150200.bed.split16794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16795 0 1 2 100 hg38.150200.bed.split16795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16796 0 1 2 100 hg38.150200.bed.split16796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16797 0 1 2 100 hg38.150200.bed.split16797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16798 0 1 2 100 hg38.150200.bed.split16798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16799 0 1 2 100 hg38.150200.bed.split16799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split168 0 1 2 100 hg38.150200.bed.split168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1680 0 1 2 100 hg38.150200.bed.split1680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16800 0 1 2 100 hg38.150200.bed.split16800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16801 0 1 2 100 hg38.150200.bed.split16801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16802 0 1 2 100 hg38.150200.bed.split16802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16803 0 1 2 100 hg38.150200.bed.split16803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16804 0 1 2 100 hg38.150200.bed.split16804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16805 0 1 2 100 hg38.150200.bed.split16805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16806 0 1 2 100 hg38.150200.bed.split16806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16807 0 1 2 100 hg38.150200.bed.split16807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16808 0 1 2 100 hg38.150200.bed.split16808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16809 0 1 2 100 hg38.150200.bed.split16809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1681 0 1 2 100 hg38.150200.bed.split1681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16810 0 1 2 100 hg38.150200.bed.split16810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16811 0 1 2 100 hg38.150200.bed.split16811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16812 0 1 2 100 hg38.150200.bed.split16812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16813 0 1 2 100 hg38.150200.bed.split16813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16814 0 1 2 100 hg38.150200.bed.split16814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16815 0 1 2 100 hg38.150200.bed.split16815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16816 0 1 2 100 hg38.150200.bed.split16816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16817 0 1 2 100 hg38.150200.bed.split16817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16818 0 1 2 100 hg38.150200.bed.split16818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16819 0 1 2 100 hg38.150200.bed.split16819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1682 0 1 2 100 hg38.150200.bed.split1682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16820 0 1 2 100 hg38.150200.bed.split16820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16821 0 1 2 100 hg38.150200.bed.split16821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16822 0 1 2 100 hg38.150200.bed.split16822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16823 0 1 2 100 hg38.150200.bed.split16823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16824 0 1 2 100 hg38.150200.bed.split16824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16825 0 1 2 100 hg38.150200.bed.split16825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16826 0 1 2 100 hg38.150200.bed.split16826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16827 0 1 2 100 hg38.150200.bed.split16827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16828 0 1 2 100 hg38.150200.bed.split16828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16829 0 1 2 100 hg38.150200.bed.split16829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1683 0 1 2 100 hg38.150200.bed.split1683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16830 0 1 2 100 hg38.150200.bed.split16830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16831 0 1 2 100 hg38.150200.bed.split16831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16832 0 1 2 100 hg38.150200.bed.split16832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16833 0 1 2 100 hg38.150200.bed.split16833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16834 0 1 2 100 hg38.150200.bed.split16834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16835 0 1 2 100 hg38.150200.bed.split16835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16836 0 1 2 100 hg38.150200.bed.split16836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16837 0 1 2 100 hg38.150200.bed.split16837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16838 0 1 2 100 hg38.150200.bed.split16838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16839 0 1 2 100 hg38.150200.bed.split16839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1684 0 1 2 100 hg38.150200.bed.split1684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16840 0 1 2 100 hg38.150200.bed.split16840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16841 0 1 2 100 hg38.150200.bed.split16841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16842 0 1 2 100 hg38.150200.bed.split16842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16843 0 1 2 100 hg38.150200.bed.split16843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16844 0 1 2 100 hg38.150200.bed.split16844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16845 0 1 2 100 hg38.150200.bed.split16845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16846 0 1 2 100 hg38.150200.bed.split16846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16847 0 1 2 100 hg38.150200.bed.split16847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16848 0 1 2 100 hg38.150200.bed.split16848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16849 0 1 2 100 hg38.150200.bed.split16849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1685 0 1 2 100 hg38.150200.bed.split1685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16850 0 1 2 100 hg38.150200.bed.split16850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16851 0 1 2 100 hg38.150200.bed.split16851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16852 0 1 2 100 hg38.150200.bed.split16852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16853 0 1 2 100 hg38.150200.bed.split16853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16854 0 1 2 100 hg38.150200.bed.split16854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16855 0 1 2 100 hg38.150200.bed.split16855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16856 0 1 2 100 hg38.150200.bed.split16856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16857 0 1 2 100 hg38.150200.bed.split16857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16858 0 1 2 100 hg38.150200.bed.split16858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16859 0 1 2 100 hg38.150200.bed.split16859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1686 0 1 2 100 hg38.150200.bed.split1686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16860 0 1 2 100 hg38.150200.bed.split16860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16861 0 1 2 100 hg38.150200.bed.split16861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16862 0 1 2 100 hg38.150200.bed.split16862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16863 0 1 2 100 hg38.150200.bed.split16863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16864 0 1 2 100 hg38.150200.bed.split16864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16865 0 1 2 100 hg38.150200.bed.split16865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16866 0 1 2 100 hg38.150200.bed.split16866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16867 0 1 2 100 hg38.150200.bed.split16867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16868 0 1 2 100 hg38.150200.bed.split16868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16869 0 1 2 100 hg38.150200.bed.split16869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1687 0 1 2 100 hg38.150200.bed.split1687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16870 0 1 2 100 hg38.150200.bed.split16870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16871 0 1 2 100 hg38.150200.bed.split16871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16872 0 1 2 100 hg38.150200.bed.split16872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16873 0 1 2 100 hg38.150200.bed.split16873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16874 0 1 2 100 hg38.150200.bed.split16874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16875 0 1 2 100 hg38.150200.bed.split16875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16876 0 1 2 100 hg38.150200.bed.split16876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16877 0 1 2 100 hg38.150200.bed.split16877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16878 0 1 2 100 hg38.150200.bed.split16878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16879 0 1 2 100 hg38.150200.bed.split16879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1688 0 1 2 100 hg38.150200.bed.split1688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16880 0 1 2 100 hg38.150200.bed.split16880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16881 0 1 2 100 hg38.150200.bed.split16881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16882 0 1 2 100 hg38.150200.bed.split16882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16883 0 1 2 100 hg38.150200.bed.split16883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16884 0 1 2 100 hg38.150200.bed.split16884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16885 0 1 2 100 hg38.150200.bed.split16885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16886 0 1 2 100 hg38.150200.bed.split16886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16887 0 1 2 100 hg38.150200.bed.split16887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16888 0 1 2 100 hg38.150200.bed.split16888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16889 0 1 2 100 hg38.150200.bed.split16889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1689 0 1 2 100 hg38.150200.bed.split1689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16890 0 1 2 100 hg38.150200.bed.split16890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16891 0 1 2 100 hg38.150200.bed.split16891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16892 0 1 2 100 hg38.150200.bed.split16892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16893 0 1 2 100 hg38.150200.bed.split16893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16894 0 1 2 100 hg38.150200.bed.split16894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16895 0 1 2 100 hg38.150200.bed.split16895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16896 0 1 2 100 hg38.150200.bed.split16896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16897 0 1 2 100 hg38.150200.bed.split16897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16898 0 1 2 100 hg38.150200.bed.split16898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16899 0 1 2 100 hg38.150200.bed.split16899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split169 0 1 2 100 hg38.150200.bed.split169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1690 0 1 2 100 hg38.150200.bed.split1690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16900 0 1 2 100 hg38.150200.bed.split16900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16901 0 1 2 100 hg38.150200.bed.split16901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16902 0 1 2 100 hg38.150200.bed.split16902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16903 0 1 2 100 hg38.150200.bed.split16903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16904 0 1 2 100 hg38.150200.bed.split16904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16905 0 1 2 100 hg38.150200.bed.split16905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16906 0 1 2 100 hg38.150200.bed.split16906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16907 0 1 2 100 hg38.150200.bed.split16907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16908 0 1 2 100 hg38.150200.bed.split16908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16909 0 1 2 100 hg38.150200.bed.split16909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1691 0 1 2 100 hg38.150200.bed.split1691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16910 0 1 2 100 hg38.150200.bed.split16910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16911 0 1 2 100 hg38.150200.bed.split16911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16912 0 1 2 100 hg38.150200.bed.split16912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16913 0 1 2 100 hg38.150200.bed.split16913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16914 0 1 2 100 hg38.150200.bed.split16914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16915 0 1 2 100 hg38.150200.bed.split16915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16916 0 1 2 100 hg38.150200.bed.split16916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16917 0 1 2 100 hg38.150200.bed.split16917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16918 0 1 2 100 hg38.150200.bed.split16918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16919 0 1 2 100 hg38.150200.bed.split16919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1692 0 1 2 100 hg38.150200.bed.split1692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16920 0 1 2 100 hg38.150200.bed.split16920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16921 0 1 2 100 hg38.150200.bed.split16921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16922 0 1 2 100 hg38.150200.bed.split16922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16923 0 1 2 100 hg38.150200.bed.split16923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16924 0 1 2 100 hg38.150200.bed.split16924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16925 0 1 2 100 hg38.150200.bed.split16925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16926 0 1 2 100 hg38.150200.bed.split16926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16927 0 1 2 100 hg38.150200.bed.split16927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16928 0 1 2 100 hg38.150200.bed.split16928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16929 0 1 2 100 hg38.150200.bed.split16929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1693 0 1 2 100 hg38.150200.bed.split1693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16930 0 1 2 100 hg38.150200.bed.split16930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16931 0 1 2 100 hg38.150200.bed.split16931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16932 0 1 2 100 hg38.150200.bed.split16932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16933 0 1 2 100 hg38.150200.bed.split16933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16934 0 1 2 100 hg38.150200.bed.split16934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16935 0 1 2 100 hg38.150200.bed.split16935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16936 0 1 2 100 hg38.150200.bed.split16936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16937 0 1 2 100 hg38.150200.bed.split16937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16938 0 1 2 100 hg38.150200.bed.split16938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16939 0 1 2 100 hg38.150200.bed.split16939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1694 0 1 2 100 hg38.150200.bed.split1694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16940 0 1 2 100 hg38.150200.bed.split16940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16941 0 1 2 100 hg38.150200.bed.split16941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16942 0 1 2 100 hg38.150200.bed.split16942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16943 0 1 2 100 hg38.150200.bed.split16943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16944 0 1 2 100 hg38.150200.bed.split16944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16945 0 1 2 100 hg38.150200.bed.split16945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16946 0 1 2 100 hg38.150200.bed.split16946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16947 0 1 2 100 hg38.150200.bed.split16947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16948 0 1 2 100 hg38.150200.bed.split16948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16949 0 1 2 100 hg38.150200.bed.split16949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1695 0 1 2 100 hg38.150200.bed.split1695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16950 0 1 2 100 hg38.150200.bed.split16950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16951 0 1 2 100 hg38.150200.bed.split16951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16952 0 1 2 100 hg38.150200.bed.split16952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16953 0 1 2 100 hg38.150200.bed.split16953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16954 0 1 2 100 hg38.150200.bed.split16954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16955 0 1 2 100 hg38.150200.bed.split16955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16956 0 1 2 100 hg38.150200.bed.split16956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16957 0 1 2 100 hg38.150200.bed.split16957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16958 0 1 2 100 hg38.150200.bed.split16958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16959 0 1 2 100 hg38.150200.bed.split16959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1696 0 1 2 100 hg38.150200.bed.split1696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16960 0 1 2 100 hg38.150200.bed.split16960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16961 0 1 2 100 hg38.150200.bed.split16961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16962 0 1 2 100 hg38.150200.bed.split16962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16963 0 1 2 100 hg38.150200.bed.split16963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16964 0 1 2 100 hg38.150200.bed.split16964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16965 0 1 2 100 hg38.150200.bed.split16965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16966 0 1 2 100 hg38.150200.bed.split16966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16967 0 1 2 100 hg38.150200.bed.split16967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16968 0 1 2 100 hg38.150200.bed.split16968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16969 0 1 2 100 hg38.150200.bed.split16969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1697 0 1 2 100 hg38.150200.bed.split1697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16970 0 1 2 100 hg38.150200.bed.split16970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16971 0 1 2 100 hg38.150200.bed.split16971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16972 0 1 2 100 hg38.150200.bed.split16972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16973 0 1 2 100 hg38.150200.bed.split16973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16974 0 1 2 100 hg38.150200.bed.split16974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16975 0 1 2 100 hg38.150200.bed.split16975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16976 0 1 2 100 hg38.150200.bed.split16976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16977 0 1 2 100 hg38.150200.bed.split16977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16978 0 1 2 100 hg38.150200.bed.split16978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16979 0 1 2 100 hg38.150200.bed.split16979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1698 0 1 2 100 hg38.150200.bed.split1698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16980 0 1 2 100 hg38.150200.bed.split16980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16981 0 1 2 100 hg38.150200.bed.split16981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16982 0 1 2 100 hg38.150200.bed.split16982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16983 0 1 2 100 hg38.150200.bed.split16983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16984 0 1 2 100 hg38.150200.bed.split16984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16985 0 1 2 100 hg38.150200.bed.split16985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16986 0 1 2 100 hg38.150200.bed.split16986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16987 0 1 2 100 hg38.150200.bed.split16987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16988 0 1 2 100 hg38.150200.bed.split16988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16989 0 1 2 100 hg38.150200.bed.split16989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1699 0 1 2 100 hg38.150200.bed.split1699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16990 0 1 2 100 hg38.150200.bed.split16990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16991 0 1 2 100 hg38.150200.bed.split16991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16992 0 1 2 100 hg38.150200.bed.split16992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16993 0 1 2 100 hg38.150200.bed.split16993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16994 0 1 2 100 hg38.150200.bed.split16994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16995 0 1 2 100 hg38.150200.bed.split16995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16996 0 1 2 100 hg38.150200.bed.split16996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16997 0 1 2 100 hg38.150200.bed.split16997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16998 0 1 2 100 hg38.150200.bed.split16998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split16999 0 1 2 100 hg38.150200.bed.split16999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17 0 1 2 100 hg38.150200.bed.split17.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split170 0 1 2 100 hg38.150200.bed.split170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1700 0 1 2 100 hg38.150200.bed.split1700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17000 0 1 2 100 hg38.150200.bed.split17000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17001 0 1 2 100 hg38.150200.bed.split17001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17002 0 1 2 100 hg38.150200.bed.split17002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17003 0 1 2 100 hg38.150200.bed.split17003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17004 0 1 2 100 hg38.150200.bed.split17004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17005 0 1 2 100 hg38.150200.bed.split17005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17006 0 1 2 100 hg38.150200.bed.split17006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17007 0 1 2 100 hg38.150200.bed.split17007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17008 0 1 2 100 hg38.150200.bed.split17008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17009 0 1 2 100 hg38.150200.bed.split17009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1701 0 1 2 100 hg38.150200.bed.split1701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17010 0 1 2 100 hg38.150200.bed.split17010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17011 0 1 2 100 hg38.150200.bed.split17011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17012 0 1 2 100 hg38.150200.bed.split17012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17013 0 1 2 100 hg38.150200.bed.split17013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17014 0 1 2 100 hg38.150200.bed.split17014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17015 0 1 2 100 hg38.150200.bed.split17015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17016 0 1 2 100 hg38.150200.bed.split17016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17017 0 1 2 100 hg38.150200.bed.split17017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17018 0 1 2 100 hg38.150200.bed.split17018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17019 0 1 2 100 hg38.150200.bed.split17019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1702 0 1 2 100 hg38.150200.bed.split1702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17020 0 1 2 100 hg38.150200.bed.split17020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17021 0 1 2 100 hg38.150200.bed.split17021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17022 0 1 2 100 hg38.150200.bed.split17022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17023 0 1 2 100 hg38.150200.bed.split17023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17024 0 1 2 100 hg38.150200.bed.split17024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17025 0 1 2 100 hg38.150200.bed.split17025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17026 0 1 2 100 hg38.150200.bed.split17026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17027 0 1 2 100 hg38.150200.bed.split17027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17028 0 1 2 100 hg38.150200.bed.split17028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17029 0 1 2 100 hg38.150200.bed.split17029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1703 0 1 2 100 hg38.150200.bed.split1703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17030 0 1 2 100 hg38.150200.bed.split17030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17031 0 1 2 100 hg38.150200.bed.split17031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17032 0 1 2 100 hg38.150200.bed.split17032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17033 0 1 2 100 hg38.150200.bed.split17033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17034 0 1 2 100 hg38.150200.bed.split17034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17035 0 1 2 100 hg38.150200.bed.split17035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17036 0 1 2 100 hg38.150200.bed.split17036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17037 0 1 2 100 hg38.150200.bed.split17037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17038 0 1 2 100 hg38.150200.bed.split17038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17039 0 1 2 100 hg38.150200.bed.split17039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1704 0 1 2 100 hg38.150200.bed.split1704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17040 0 1 2 100 hg38.150200.bed.split17040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17041 0 1 2 100 hg38.150200.bed.split17041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17042 0 1 2 100 hg38.150200.bed.split17042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17043 0 1 2 100 hg38.150200.bed.split17043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17044 0 1 2 100 hg38.150200.bed.split17044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17045 0 1 2 100 hg38.150200.bed.split17045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17046 0 1 2 100 hg38.150200.bed.split17046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17047 0 1 2 100 hg38.150200.bed.split17047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17048 0 1 2 100 hg38.150200.bed.split17048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17049 0 1 2 100 hg38.150200.bed.split17049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1705 0 1 2 100 hg38.150200.bed.split1705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17050 0 1 2 100 hg38.150200.bed.split17050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17051 0 1 2 100 hg38.150200.bed.split17051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17052 0 1 2 100 hg38.150200.bed.split17052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17053 0 1 2 100 hg38.150200.bed.split17053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17054 0 1 2 100 hg38.150200.bed.split17054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17055 0 1 2 100 hg38.150200.bed.split17055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17056 0 1 2 100 hg38.150200.bed.split17056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17057 0 1 2 100 hg38.150200.bed.split17057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17058 0 1 2 100 hg38.150200.bed.split17058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17059 0 1 2 100 hg38.150200.bed.split17059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1706 0 1 2 100 hg38.150200.bed.split1706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17060 0 1 2 100 hg38.150200.bed.split17060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17061 0 1 2 100 hg38.150200.bed.split17061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17062 0 1 2 100 hg38.150200.bed.split17062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17063 0 1 2 100 hg38.150200.bed.split17063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17064 0 1 2 100 hg38.150200.bed.split17064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17065 0 1 2 100 hg38.150200.bed.split17065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17066 0 1 2 100 hg38.150200.bed.split17066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17067 0 1 2 100 hg38.150200.bed.split17067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17068 0 1 2 100 hg38.150200.bed.split17068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17069 0 1 2 100 hg38.150200.bed.split17069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1707 0 1 2 100 hg38.150200.bed.split1707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17070 0 1 2 100 hg38.150200.bed.split17070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17071 0 1 2 100 hg38.150200.bed.split17071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17072 0 1 2 100 hg38.150200.bed.split17072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17073 0 1 2 100 hg38.150200.bed.split17073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17074 0 1 2 100 hg38.150200.bed.split17074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17075 0 1 2 100 hg38.150200.bed.split17075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17076 0 1 2 100 hg38.150200.bed.split17076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17077 0 1 2 100 hg38.150200.bed.split17077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17078 0 1 2 100 hg38.150200.bed.split17078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17079 0 1 2 100 hg38.150200.bed.split17079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1708 0 1 2 100 hg38.150200.bed.split1708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17080 0 1 2 100 hg38.150200.bed.split17080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17081 0 1 2 100 hg38.150200.bed.split17081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17082 0 1 2 100 hg38.150200.bed.split17082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17083 0 1 2 100 hg38.150200.bed.split17083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17084 0 1 2 100 hg38.150200.bed.split17084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17085 0 1 2 100 hg38.150200.bed.split17085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17086 0 1 2 100 hg38.150200.bed.split17086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17087 0 1 2 100 hg38.150200.bed.split17087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17088 0 1 2 100 hg38.150200.bed.split17088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17089 0 1 2 100 hg38.150200.bed.split17089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1709 0 1 2 100 hg38.150200.bed.split1709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17090 0 1 2 100 hg38.150200.bed.split17090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17091 0 1 2 100 hg38.150200.bed.split17091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17092 0 1 2 100 hg38.150200.bed.split17092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17093 0 1 2 100 hg38.150200.bed.split17093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17094 0 1 2 100 hg38.150200.bed.split17094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17095 0 1 2 100 hg38.150200.bed.split17095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17096 0 1 2 100 hg38.150200.bed.split17096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17097 0 1 2 100 hg38.150200.bed.split17097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17098 0 1 2 100 hg38.150200.bed.split17098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17099 0 1 2 100 hg38.150200.bed.split17099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split171 0 1 2 100 hg38.150200.bed.split171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1710 0 1 2 100 hg38.150200.bed.split1710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17100 0 1 2 100 hg38.150200.bed.split17100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17101 0 1 2 100 hg38.150200.bed.split17101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17102 0 1 2 100 hg38.150200.bed.split17102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17103 0 1 2 100 hg38.150200.bed.split17103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17104 0 1 2 100 hg38.150200.bed.split17104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17105 0 1 2 100 hg38.150200.bed.split17105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17106 0 1 2 100 hg38.150200.bed.split17106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17107 0 1 2 100 hg38.150200.bed.split17107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17108 0 1 2 100 hg38.150200.bed.split17108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17109 0 1 2 100 hg38.150200.bed.split17109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1711 0 1 2 100 hg38.150200.bed.split1711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17110 0 1 2 100 hg38.150200.bed.split17110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17111 0 1 2 100 hg38.150200.bed.split17111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17112 0 1 2 100 hg38.150200.bed.split17112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17113 0 1 2 100 hg38.150200.bed.split17113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17114 0 1 2 100 hg38.150200.bed.split17114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17115 0 1 2 100 hg38.150200.bed.split17115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17116 0 1 2 100 hg38.150200.bed.split17116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17117 0 1 2 100 hg38.150200.bed.split17117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17118 0 1 2 100 hg38.150200.bed.split17118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17119 0 1 2 100 hg38.150200.bed.split17119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1712 0 1 2 100 hg38.150200.bed.split1712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17120 0 1 2 100 hg38.150200.bed.split17120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17121 0 1 2 100 hg38.150200.bed.split17121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17122 0 1 2 100 hg38.150200.bed.split17122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17123 0 1 2 100 hg38.150200.bed.split17123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17124 0 1 2 100 hg38.150200.bed.split17124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17125 0 1 2 100 hg38.150200.bed.split17125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17126 0 1 2 100 hg38.150200.bed.split17126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17127 0 1 2 100 hg38.150200.bed.split17127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17128 0 1 2 100 hg38.150200.bed.split17128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17129 0 1 2 100 hg38.150200.bed.split17129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1713 0 1 2 100 hg38.150200.bed.split1713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17130 0 1 2 100 hg38.150200.bed.split17130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17131 0 1 2 100 hg38.150200.bed.split17131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17132 0 1 2 100 hg38.150200.bed.split17132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17133 0 1 2 100 hg38.150200.bed.split17133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17134 0 1 2 100 hg38.150200.bed.split17134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17135 0 1 2 100 hg38.150200.bed.split17135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17136 0 1 2 100 hg38.150200.bed.split17136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17137 0 1 2 100 hg38.150200.bed.split17137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17138 0 1 2 100 hg38.150200.bed.split17138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17139 0 1 2 100 hg38.150200.bed.split17139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1714 0 1 2 100 hg38.150200.bed.split1714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17140 0 1 2 100 hg38.150200.bed.split17140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17141 0 1 2 100 hg38.150200.bed.split17141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17142 0 1 2 100 hg38.150200.bed.split17142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17143 0 1 2 100 hg38.150200.bed.split17143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17144 0 1 2 100 hg38.150200.bed.split17144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17145 0 1 2 100 hg38.150200.bed.split17145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17146 0 1 2 100 hg38.150200.bed.split17146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17147 0 1 2 100 hg38.150200.bed.split17147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17148 0 1 2 100 hg38.150200.bed.split17148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17149 0 1 2 100 hg38.150200.bed.split17149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1715 0 1 2 100 hg38.150200.bed.split1715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17150 0 1 2 100 hg38.150200.bed.split17150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17151 0 1 2 100 hg38.150200.bed.split17151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17152 0 1 2 100 hg38.150200.bed.split17152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17153 0 1 2 100 hg38.150200.bed.split17153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17154 0 1 2 100 hg38.150200.bed.split17154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17155 0 1 2 100 hg38.150200.bed.split17155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17156 0 1 2 100 hg38.150200.bed.split17156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17157 0 1 2 100 hg38.150200.bed.split17157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17158 0 1 2 100 hg38.150200.bed.split17158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17159 0 1 2 100 hg38.150200.bed.split17159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1716 0 1 2 100 hg38.150200.bed.split1716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17160 0 1 2 100 hg38.150200.bed.split17160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17161 0 1 2 100 hg38.150200.bed.split17161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17162 0 1 2 100 hg38.150200.bed.split17162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17163 0 1 2 100 hg38.150200.bed.split17163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17164 0 1 2 100 hg38.150200.bed.split17164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17165 0 1 2 100 hg38.150200.bed.split17165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17166 0 1 2 100 hg38.150200.bed.split17166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17167 0 1 2 100 hg38.150200.bed.split17167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17168 0 1 2 100 hg38.150200.bed.split17168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17169 0 1 2 100 hg38.150200.bed.split17169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1717 0 1 2 100 hg38.150200.bed.split1717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17170 0 1 2 100 hg38.150200.bed.split17170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17171 0 1 2 100 hg38.150200.bed.split17171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17172 0 1 2 100 hg38.150200.bed.split17172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17173 0 1 2 100 hg38.150200.bed.split17173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17174 0 1 2 100 hg38.150200.bed.split17174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17175 0 1 2 100 hg38.150200.bed.split17175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17176 0 1 2 100 hg38.150200.bed.split17176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17177 0 1 2 100 hg38.150200.bed.split17177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17178 0 1 2 100 hg38.150200.bed.split17178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17179 0 1 2 100 hg38.150200.bed.split17179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1718 0 1 2 100 hg38.150200.bed.split1718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17180 0 1 2 100 hg38.150200.bed.split17180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17181 0 1 2 100 hg38.150200.bed.split17181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17182 0 1 2 100 hg38.150200.bed.split17182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17183 0 1 2 100 hg38.150200.bed.split17183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17184 0 1 2 100 hg38.150200.bed.split17184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17185 0 1 2 100 hg38.150200.bed.split17185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17186 0 1 2 100 hg38.150200.bed.split17186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17187 0 1 2 100 hg38.150200.bed.split17187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17188 0 1 2 100 hg38.150200.bed.split17188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17189 0 1 2 100 hg38.150200.bed.split17189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1719 0 1 2 100 hg38.150200.bed.split1719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17190 0 1 2 100 hg38.150200.bed.split17190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17191 0 1 2 100 hg38.150200.bed.split17191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17192 0 1 2 100 hg38.150200.bed.split17192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17193 0 1 2 100 hg38.150200.bed.split17193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17194 0 1 2 100 hg38.150200.bed.split17194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17195 0 1 2 100 hg38.150200.bed.split17195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17196 0 1 2 100 hg38.150200.bed.split17196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17197 0 1 2 100 hg38.150200.bed.split17197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17198 0 1 2 100 hg38.150200.bed.split17198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17199 0 1 2 100 hg38.150200.bed.split17199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split172 0 1 2 100 hg38.150200.bed.split172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1720 0 1 2 100 hg38.150200.bed.split1720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17200 0 1 2 100 hg38.150200.bed.split17200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17201 0 1 2 100 hg38.150200.bed.split17201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17202 0 1 2 100 hg38.150200.bed.split17202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17203 0 1 2 100 hg38.150200.bed.split17203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17204 0 1 2 100 hg38.150200.bed.split17204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17205 0 1 2 100 hg38.150200.bed.split17205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17206 0 1 2 100 hg38.150200.bed.split17206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17207 0 1 2 100 hg38.150200.bed.split17207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17208 0 1 2 100 hg38.150200.bed.split17208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17209 0 1 2 100 hg38.150200.bed.split17209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1721 0 1 2 100 hg38.150200.bed.split1721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17210 0 1 2 100 hg38.150200.bed.split17210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17211 0 1 2 100 hg38.150200.bed.split17211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17212 0 1 2 100 hg38.150200.bed.split17212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17213 0 1 2 100 hg38.150200.bed.split17213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17214 0 1 2 100 hg38.150200.bed.split17214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17215 0 1 2 100 hg38.150200.bed.split17215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17216 0 1 2 100 hg38.150200.bed.split17216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17217 0 1 2 100 hg38.150200.bed.split17217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17218 0 1 2 100 hg38.150200.bed.split17218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17219 0 1 2 100 hg38.150200.bed.split17219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1722 0 1 2 100 hg38.150200.bed.split1722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17220 0 1 2 100 hg38.150200.bed.split17220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17221 0 1 2 100 hg38.150200.bed.split17221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17222 0 1 2 100 hg38.150200.bed.split17222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17223 0 1 2 100 hg38.150200.bed.split17223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17224 0 1 2 100 hg38.150200.bed.split17224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17225 0 1 2 100 hg38.150200.bed.split17225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17226 0 1 2 100 hg38.150200.bed.split17226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17227 0 1 2 100 hg38.150200.bed.split17227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17228 0 1 2 100 hg38.150200.bed.split17228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17229 0 1 2 100 hg38.150200.bed.split17229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1723 0 1 2 100 hg38.150200.bed.split1723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17230 0 1 2 100 hg38.150200.bed.split17230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17231 0 1 2 100 hg38.150200.bed.split17231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17232 0 1 2 100 hg38.150200.bed.split17232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17233 0 1 2 100 hg38.150200.bed.split17233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17234 0 1 2 100 hg38.150200.bed.split17234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17235 0 1 2 100 hg38.150200.bed.split17235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17236 0 1 2 100 hg38.150200.bed.split17236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17237 0 1 2 100 hg38.150200.bed.split17237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17238 0 1 2 100 hg38.150200.bed.split17238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17239 0 1 2 100 hg38.150200.bed.split17239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1724 0 1 2 100 hg38.150200.bed.split1724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17240 0 1 2 100 hg38.150200.bed.split17240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17241 0 1 2 100 hg38.150200.bed.split17241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17242 0 1 2 100 hg38.150200.bed.split17242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17243 0 1 2 100 hg38.150200.bed.split17243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17244 0 1 2 100 hg38.150200.bed.split17244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17245 0 1 2 100 hg38.150200.bed.split17245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17246 0 1 2 100 hg38.150200.bed.split17246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17247 0 1 2 100 hg38.150200.bed.split17247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17248 0 1 2 100 hg38.150200.bed.split17248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17249 0 1 2 100 hg38.150200.bed.split17249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1725 0 1 2 100 hg38.150200.bed.split1725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17250 0 1 2 100 hg38.150200.bed.split17250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17251 0 1 2 100 hg38.150200.bed.split17251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17252 0 1 2 100 hg38.150200.bed.split17252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17253 0 1 2 100 hg38.150200.bed.split17253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17254 0 1 2 100 hg38.150200.bed.split17254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17255 0 1 2 100 hg38.150200.bed.split17255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17256 0 1 2 100 hg38.150200.bed.split17256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17257 0 1 2 100 hg38.150200.bed.split17257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17258 0 1 2 100 hg38.150200.bed.split17258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17259 0 1 2 100 hg38.150200.bed.split17259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1726 0 1 2 100 hg38.150200.bed.split1726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17260 0 1 2 100 hg38.150200.bed.split17260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17261 0 1 2 100 hg38.150200.bed.split17261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17262 0 1 2 100 hg38.150200.bed.split17262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17263 0 1 2 100 hg38.150200.bed.split17263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17264 0 1 2 100 hg38.150200.bed.split17264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17265 0 1 2 100 hg38.150200.bed.split17265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17266 0 1 2 100 hg38.150200.bed.split17266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17267 0 1 2 100 hg38.150200.bed.split17267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17268 0 1 2 100 hg38.150200.bed.split17268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17269 0 1 2 100 hg38.150200.bed.split17269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1727 0 1 2 100 hg38.150200.bed.split1727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17270 0 1 2 100 hg38.150200.bed.split17270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17271 0 1 2 100 hg38.150200.bed.split17271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17272 0 1 2 100 hg38.150200.bed.split17272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17273 0 1 2 100 hg38.150200.bed.split17273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17274 0 1 2 100 hg38.150200.bed.split17274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17275 0 1 2 100 hg38.150200.bed.split17275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17276 0 1 2 100 hg38.150200.bed.split17276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17277 0 1 2 100 hg38.150200.bed.split17277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17278 0 1 2 100 hg38.150200.bed.split17278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17279 0 1 2 100 hg38.150200.bed.split17279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1728 0 1 2 100 hg38.150200.bed.split1728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17280 0 1 2 100 hg38.150200.bed.split17280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17281 0 1 2 100 hg38.150200.bed.split17281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17282 0 1 2 100 hg38.150200.bed.split17282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17283 0 1 2 100 hg38.150200.bed.split17283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17284 0 1 2 100 hg38.150200.bed.split17284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17285 0 1 2 100 hg38.150200.bed.split17285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17286 0 1 2 100 hg38.150200.bed.split17286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17287 0 1 2 100 hg38.150200.bed.split17287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17288 0 1 2 100 hg38.150200.bed.split17288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17289 0 1 2 100 hg38.150200.bed.split17289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1729 0 1 2 100 hg38.150200.bed.split1729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17290 0 1 2 100 hg38.150200.bed.split17290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17291 0 1 2 100 hg38.150200.bed.split17291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17292 0 1 2 100 hg38.150200.bed.split17292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17293 0 1 2 100 hg38.150200.bed.split17293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17294 0 1 2 100 hg38.150200.bed.split17294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17295 0 1 2 100 hg38.150200.bed.split17295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17296 0 1 2 100 hg38.150200.bed.split17296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17297 0 1 2 100 hg38.150200.bed.split17297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17298 0 1 2 100 hg38.150200.bed.split17298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17299 0 1 2 100 hg38.150200.bed.split17299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split173 0 1 2 100 hg38.150200.bed.split173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1730 0 1 2 100 hg38.150200.bed.split1730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17300 0 1 2 100 hg38.150200.bed.split17300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17301 0 1 2 100 hg38.150200.bed.split17301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17302 0 1 2 100 hg38.150200.bed.split17302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17303 0 1 2 100 hg38.150200.bed.split17303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17304 0 1 2 100 hg38.150200.bed.split17304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17305 0 1 2 100 hg38.150200.bed.split17305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17306 0 1 2 100 hg38.150200.bed.split17306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17307 0 1 2 100 hg38.150200.bed.split17307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17308 0 1 2 100 hg38.150200.bed.split17308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17309 0 1 2 100 hg38.150200.bed.split17309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1731 0 1 2 100 hg38.150200.bed.split1731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17310 0 1 2 100 hg38.150200.bed.split17310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17311 0 1 2 100 hg38.150200.bed.split17311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17312 0 1 2 100 hg38.150200.bed.split17312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17313 0 1 2 100 hg38.150200.bed.split17313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17314 0 1 2 100 hg38.150200.bed.split17314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17315 0 1 2 100 hg38.150200.bed.split17315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17316 0 1 2 100 hg38.150200.bed.split17316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17317 0 1 2 100 hg38.150200.bed.split17317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17318 0 1 2 100 hg38.150200.bed.split17318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17319 0 1 2 100 hg38.150200.bed.split17319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1732 0 1 2 100 hg38.150200.bed.split1732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17320 0 1 2 100 hg38.150200.bed.split17320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17321 0 1 2 100 hg38.150200.bed.split17321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17322 0 1 2 100 hg38.150200.bed.split17322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17323 0 1 2 100 hg38.150200.bed.split17323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17324 0 1 2 100 hg38.150200.bed.split17324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17325 0 1 2 100 hg38.150200.bed.split17325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17326 0 1 2 100 hg38.150200.bed.split17326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17327 0 1 2 100 hg38.150200.bed.split17327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17328 0 1 2 100 hg38.150200.bed.split17328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17329 0 1 2 100 hg38.150200.bed.split17329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1733 0 1 2 100 hg38.150200.bed.split1733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17330 0 1 2 100 hg38.150200.bed.split17330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17331 0 1 2 100 hg38.150200.bed.split17331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17332 0 1 2 100 hg38.150200.bed.split17332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17333 0 1 2 100 hg38.150200.bed.split17333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17334 0 1 2 100 hg38.150200.bed.split17334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17335 0 1 2 100 hg38.150200.bed.split17335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17336 0 1 2 100 hg38.150200.bed.split17336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17337 0 1 2 100 hg38.150200.bed.split17337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17338 0 1 2 100 hg38.150200.bed.split17338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17339 0 1 2 100 hg38.150200.bed.split17339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1734 0 1 2 100 hg38.150200.bed.split1734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17340 0 1 2 100 hg38.150200.bed.split17340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17341 0 1 2 100 hg38.150200.bed.split17341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17342 0 1 2 100 hg38.150200.bed.split17342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17343 0 1 2 100 hg38.150200.bed.split17343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17344 0 1 2 100 hg38.150200.bed.split17344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17345 0 1 2 100 hg38.150200.bed.split17345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17346 0 1 2 100 hg38.150200.bed.split17346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17347 0 1 2 100 hg38.150200.bed.split17347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17348 0 1 2 100 hg38.150200.bed.split17348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17349 0 1 2 100 hg38.150200.bed.split17349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1735 0 1 2 100 hg38.150200.bed.split1735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17350 0 1 2 100 hg38.150200.bed.split17350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17351 0 1 2 100 hg38.150200.bed.split17351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17352 0 1 2 100 hg38.150200.bed.split17352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17353 0 1 2 100 hg38.150200.bed.split17353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17354 0 1 2 100 hg38.150200.bed.split17354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17355 0 1 2 100 hg38.150200.bed.split17355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17356 0 1 2 100 hg38.150200.bed.split17356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17357 0 1 2 100 hg38.150200.bed.split17357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17358 0 1 2 100 hg38.150200.bed.split17358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17359 0 1 2 100 hg38.150200.bed.split17359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1736 0 1 2 100 hg38.150200.bed.split1736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17360 0 1 2 100 hg38.150200.bed.split17360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17361 0 1 2 100 hg38.150200.bed.split17361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17362 0 1 2 100 hg38.150200.bed.split17362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17363 0 1 2 100 hg38.150200.bed.split17363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17364 0 1 2 100 hg38.150200.bed.split17364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17365 0 1 2 100 hg38.150200.bed.split17365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17366 0 1 2 100 hg38.150200.bed.split17366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17367 0 1 2 100 hg38.150200.bed.split17367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17368 0 1 2 100 hg38.150200.bed.split17368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17369 0 1 2 100 hg38.150200.bed.split17369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1737 0 1 2 100 hg38.150200.bed.split1737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17370 0 1 2 100 hg38.150200.bed.split17370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17371 0 1 2 100 hg38.150200.bed.split17371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17372 0 1 2 100 hg38.150200.bed.split17372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17373 0 1 2 100 hg38.150200.bed.split17373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17374 0 1 2 100 hg38.150200.bed.split17374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17375 0 1 2 100 hg38.150200.bed.split17375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17376 0 1 2 100 hg38.150200.bed.split17376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17377 0 1 2 100 hg38.150200.bed.split17377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17378 0 1 2 100 hg38.150200.bed.split17378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17379 0 1 2 100 hg38.150200.bed.split17379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1738 0 1 2 100 hg38.150200.bed.split1738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17380 0 1 2 100 hg38.150200.bed.split17380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17381 0 1 2 100 hg38.150200.bed.split17381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17382 0 1 2 100 hg38.150200.bed.split17382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17383 0 1 2 100 hg38.150200.bed.split17383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17384 0 1 2 100 hg38.150200.bed.split17384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17385 0 1 2 100 hg38.150200.bed.split17385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17386 0 1 2 100 hg38.150200.bed.split17386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17387 0 1 2 100 hg38.150200.bed.split17387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17388 0 1 2 100 hg38.150200.bed.split17388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17389 0 1 2 100 hg38.150200.bed.split17389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1739 0 1 2 100 hg38.150200.bed.split1739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17390 0 1 2 100 hg38.150200.bed.split17390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17391 0 1 2 100 hg38.150200.bed.split17391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17392 0 1 2 100 hg38.150200.bed.split17392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17393 0 1 2 100 hg38.150200.bed.split17393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17394 0 1 2 100 hg38.150200.bed.split17394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17395 0 1 2 100 hg38.150200.bed.split17395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17396 0 1 2 100 hg38.150200.bed.split17396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17397 0 1 2 100 hg38.150200.bed.split17397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17398 0 1 2 100 hg38.150200.bed.split17398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17399 0 1 2 100 hg38.150200.bed.split17399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split174 0 1 2 100 hg38.150200.bed.split174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1740 0 1 2 100 hg38.150200.bed.split1740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17400 0 1 2 100 hg38.150200.bed.split17400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17401 0 1 2 100 hg38.150200.bed.split17401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17402 0 1 2 100 hg38.150200.bed.split17402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17403 0 1 2 100 hg38.150200.bed.split17403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17404 0 1 2 100 hg38.150200.bed.split17404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17405 0 1 2 100 hg38.150200.bed.split17405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17406 0 1 2 100 hg38.150200.bed.split17406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17407 0 1 2 100 hg38.150200.bed.split17407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17408 0 1 2 100 hg38.150200.bed.split17408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17409 0 1 2 100 hg38.150200.bed.split17409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1741 0 1 2 100 hg38.150200.bed.split1741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17410 0 1 2 100 hg38.150200.bed.split17410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17411 0 1 2 100 hg38.150200.bed.split17411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17412 0 1 2 100 hg38.150200.bed.split17412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17413 0 1 2 100 hg38.150200.bed.split17413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17414 0 1 2 100 hg38.150200.bed.split17414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17415 0 1 2 100 hg38.150200.bed.split17415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17416 0 1 2 100 hg38.150200.bed.split17416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17417 0 1 2 100 hg38.150200.bed.split17417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17418 0 1 2 100 hg38.150200.bed.split17418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17419 0 1 2 100 hg38.150200.bed.split17419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1742 0 1 2 100 hg38.150200.bed.split1742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17420 0 1 2 100 hg38.150200.bed.split17420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17421 0 1 2 100 hg38.150200.bed.split17421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17422 0 1 2 100 hg38.150200.bed.split17422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17423 0 1 2 100 hg38.150200.bed.split17423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17424 0 1 2 100 hg38.150200.bed.split17424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17425 0 1 2 100 hg38.150200.bed.split17425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17426 0 1 2 100 hg38.150200.bed.split17426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17427 0 1 2 100 hg38.150200.bed.split17427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17428 0 1 2 100 hg38.150200.bed.split17428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17429 0 1 2 100 hg38.150200.bed.split17429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1743 0 1 2 100 hg38.150200.bed.split1743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17430 0 1 2 100 hg38.150200.bed.split17430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17431 0 1 2 100 hg38.150200.bed.split17431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17432 0 1 2 100 hg38.150200.bed.split17432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17433 0 1 2 100 hg38.150200.bed.split17433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17434 0 1 2 100 hg38.150200.bed.split17434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17435 0 1 2 100 hg38.150200.bed.split17435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17436 0 1 2 100 hg38.150200.bed.split17436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17437 0 1 2 100 hg38.150200.bed.split17437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17438 0 1 2 100 hg38.150200.bed.split17438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17439 0 1 2 100 hg38.150200.bed.split17439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1744 0 1 2 100 hg38.150200.bed.split1744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17440 0 1 2 100 hg38.150200.bed.split17440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17441 0 1 2 100 hg38.150200.bed.split17441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17442 0 1 2 100 hg38.150200.bed.split17442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17443 0 1 2 100 hg38.150200.bed.split17443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17444 0 1 2 100 hg38.150200.bed.split17444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17445 0 1 2 100 hg38.150200.bed.split17445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17446 0 1 2 100 hg38.150200.bed.split17446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17447 0 1 2 100 hg38.150200.bed.split17447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17448 0 1 2 100 hg38.150200.bed.split17448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17449 0 1 2 100 hg38.150200.bed.split17449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1745 0 1 2 100 hg38.150200.bed.split1745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17450 0 1 2 100 hg38.150200.bed.split17450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17451 0 1 2 100 hg38.150200.bed.split17451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17452 0 1 2 100 hg38.150200.bed.split17452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17453 0 1 2 100 hg38.150200.bed.split17453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17454 0 1 2 100 hg38.150200.bed.split17454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17455 0 1 2 100 hg38.150200.bed.split17455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17456 0 1 2 100 hg38.150200.bed.split17456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17457 0 1 2 100 hg38.150200.bed.split17457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17458 0 1 2 100 hg38.150200.bed.split17458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17459 0 1 2 100 hg38.150200.bed.split17459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1746 0 1 2 100 hg38.150200.bed.split1746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17460 0 1 2 100 hg38.150200.bed.split17460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17461 0 1 2 100 hg38.150200.bed.split17461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17462 0 1 2 100 hg38.150200.bed.split17462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17463 0 1 2 100 hg38.150200.bed.split17463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17464 0 1 2 100 hg38.150200.bed.split17464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17465 0 1 2 100 hg38.150200.bed.split17465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17466 0 1 2 100 hg38.150200.bed.split17466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17467 0 1 2 100 hg38.150200.bed.split17467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17468 0 1 2 100 hg38.150200.bed.split17468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17469 0 1 2 100 hg38.150200.bed.split17469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1747 0 1 2 100 hg38.150200.bed.split1747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17470 0 1 2 100 hg38.150200.bed.split17470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17471 0 1 2 100 hg38.150200.bed.split17471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17472 0 1 2 100 hg38.150200.bed.split17472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17473 0 1 2 100 hg38.150200.bed.split17473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17474 0 1 2 100 hg38.150200.bed.split17474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17475 0 1 2 100 hg38.150200.bed.split17475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17476 0 1 2 100 hg38.150200.bed.split17476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17477 0 1 2 100 hg38.150200.bed.split17477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17478 0 1 2 100 hg38.150200.bed.split17478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17479 0 1 2 100 hg38.150200.bed.split17479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1748 0 1 2 100 hg38.150200.bed.split1748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17480 0 1 2 100 hg38.150200.bed.split17480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17481 0 1 2 100 hg38.150200.bed.split17481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17482 0 1 2 100 hg38.150200.bed.split17482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17483 0 1 2 100 hg38.150200.bed.split17483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17484 0 1 2 100 hg38.150200.bed.split17484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17485 0 1 2 100 hg38.150200.bed.split17485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17486 0 1 2 100 hg38.150200.bed.split17486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17487 0 1 2 100 hg38.150200.bed.split17487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17488 0 1 2 100 hg38.150200.bed.split17488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17489 0 1 2 100 hg38.150200.bed.split17489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1749 0 1 2 100 hg38.150200.bed.split1749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17490 0 1 2 100 hg38.150200.bed.split17490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17491 0 1 2 100 hg38.150200.bed.split17491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17492 0 1 2 100 hg38.150200.bed.split17492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17493 0 1 2 100 hg38.150200.bed.split17493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17494 0 1 2 100 hg38.150200.bed.split17494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17495 0 1 2 100 hg38.150200.bed.split17495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17496 0 1 2 100 hg38.150200.bed.split17496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17497 0 1 2 100 hg38.150200.bed.split17497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17498 0 1 2 100 hg38.150200.bed.split17498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17499 0 1 2 100 hg38.150200.bed.split17499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split175 0 1 2 100 hg38.150200.bed.split175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1750 0 1 2 100 hg38.150200.bed.split1750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17500 0 1 2 100 hg38.150200.bed.split17500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17501 0 1 2 100 hg38.150200.bed.split17501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17502 0 1 2 100 hg38.150200.bed.split17502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17503 0 1 2 100 hg38.150200.bed.split17503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17504 0 1 2 100 hg38.150200.bed.split17504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17505 0 1 2 100 hg38.150200.bed.split17505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17506 0 1 2 100 hg38.150200.bed.split17506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17507 0 1 2 100 hg38.150200.bed.split17507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17508 0 1 2 100 hg38.150200.bed.split17508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17509 0 1 2 100 hg38.150200.bed.split17509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1751 0 1 2 100 hg38.150200.bed.split1751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17510 0 1 2 100 hg38.150200.bed.split17510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17511 0 1 2 100 hg38.150200.bed.split17511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17512 0 1 2 100 hg38.150200.bed.split17512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17513 0 1 2 100 hg38.150200.bed.split17513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17514 0 1 2 100 hg38.150200.bed.split17514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17515 0 1 2 100 hg38.150200.bed.split17515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17516 0 1 2 100 hg38.150200.bed.split17516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17517 0 1 2 100 hg38.150200.bed.split17517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17518 0 1 2 100 hg38.150200.bed.split17518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17519 0 1 2 100 hg38.150200.bed.split17519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1752 0 1 2 100 hg38.150200.bed.split1752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17520 0 1 2 100 hg38.150200.bed.split17520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17521 0 1 2 100 hg38.150200.bed.split17521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17522 0 1 2 100 hg38.150200.bed.split17522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17523 0 1 2 100 hg38.150200.bed.split17523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17524 0 1 2 100 hg38.150200.bed.split17524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17525 0 1 2 100 hg38.150200.bed.split17525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17526 0 1 2 100 hg38.150200.bed.split17526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17527 0 1 2 100 hg38.150200.bed.split17527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17528 0 1 2 100 hg38.150200.bed.split17528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17529 0 1 2 100 hg38.150200.bed.split17529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1753 0 1 2 100 hg38.150200.bed.split1753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17530 0 1 2 100 hg38.150200.bed.split17530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17531 0 1 2 100 hg38.150200.bed.split17531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17532 0 1 2 100 hg38.150200.bed.split17532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17533 0 1 2 100 hg38.150200.bed.split17533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17534 0 1 2 100 hg38.150200.bed.split17534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17535 0 1 2 100 hg38.150200.bed.split17535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17536 0 1 2 100 hg38.150200.bed.split17536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17537 0 1 2 100 hg38.150200.bed.split17537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17538 0 1 2 100 hg38.150200.bed.split17538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17539 0 1 2 100 hg38.150200.bed.split17539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1754 0 1 2 100 hg38.150200.bed.split1754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17540 0 1 2 100 hg38.150200.bed.split17540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17541 0 1 2 100 hg38.150200.bed.split17541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17542 0 1 2 100 hg38.150200.bed.split17542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17543 0 1 2 100 hg38.150200.bed.split17543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17544 0 1 2 100 hg38.150200.bed.split17544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17545 0 1 2 100 hg38.150200.bed.split17545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17546 0 1 2 100 hg38.150200.bed.split17546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17547 0 1 2 100 hg38.150200.bed.split17547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17548 0 1 2 100 hg38.150200.bed.split17548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17549 0 1 2 100 hg38.150200.bed.split17549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1755 0 1 2 100 hg38.150200.bed.split1755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17550 0 1 2 100 hg38.150200.bed.split17550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17551 0 1 2 100 hg38.150200.bed.split17551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17552 0 1 2 100 hg38.150200.bed.split17552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17553 0 1 2 100 hg38.150200.bed.split17553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17554 0 1 2 100 hg38.150200.bed.split17554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17555 0 1 2 100 hg38.150200.bed.split17555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17556 0 1 2 100 hg38.150200.bed.split17556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17557 0 1 2 100 hg38.150200.bed.split17557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17558 0 1 2 100 hg38.150200.bed.split17558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17559 0 1 2 100 hg38.150200.bed.split17559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1756 0 1 2 100 hg38.150200.bed.split1756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17560 0 1 2 100 hg38.150200.bed.split17560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17561 0 1 2 100 hg38.150200.bed.split17561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17562 0 1 2 100 hg38.150200.bed.split17562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17563 0 1 2 100 hg38.150200.bed.split17563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17564 0 1 2 100 hg38.150200.bed.split17564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17565 0 1 2 100 hg38.150200.bed.split17565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17566 0 1 2 100 hg38.150200.bed.split17566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17567 0 1 2 100 hg38.150200.bed.split17567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17568 0 1 2 100 hg38.150200.bed.split17568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17569 0 1 2 100 hg38.150200.bed.split17569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1757 0 1 2 100 hg38.150200.bed.split1757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17570 0 1 2 100 hg38.150200.bed.split17570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17571 0 1 2 100 hg38.150200.bed.split17571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17572 0 1 2 100 hg38.150200.bed.split17572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17573 0 1 2 100 hg38.150200.bed.split17573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17574 0 1 2 100 hg38.150200.bed.split17574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17575 0 1 2 100 hg38.150200.bed.split17575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17576 0 1 2 100 hg38.150200.bed.split17576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17577 0 1 2 100 hg38.150200.bed.split17577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17578 0 1 2 100 hg38.150200.bed.split17578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17579 0 1 2 100 hg38.150200.bed.split17579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1758 0 1 2 100 hg38.150200.bed.split1758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17580 0 1 2 100 hg38.150200.bed.split17580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17581 0 1 2 100 hg38.150200.bed.split17581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17582 0 1 2 100 hg38.150200.bed.split17582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17583 0 1 2 100 hg38.150200.bed.split17583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17584 0 1 2 100 hg38.150200.bed.split17584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17585 0 1 2 100 hg38.150200.bed.split17585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17586 0 1 2 100 hg38.150200.bed.split17586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17587 0 1 2 100 hg38.150200.bed.split17587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17588 0 1 2 100 hg38.150200.bed.split17588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17589 0 1 2 100 hg38.150200.bed.split17589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1759 0 1 2 100 hg38.150200.bed.split1759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17590 0 1 2 100 hg38.150200.bed.split17590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17591 0 1 2 100 hg38.150200.bed.split17591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17592 0 1 2 100 hg38.150200.bed.split17592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17593 0 1 2 100 hg38.150200.bed.split17593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17594 0 1 2 100 hg38.150200.bed.split17594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17595 0 1 2 100 hg38.150200.bed.split17595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17596 0 1 2 100 hg38.150200.bed.split17596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17597 0 1 2 100 hg38.150200.bed.split17597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17598 0 1 2 100 hg38.150200.bed.split17598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17599 0 1 2 100 hg38.150200.bed.split17599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split176 0 1 2 100 hg38.150200.bed.split176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1760 0 1 2 100 hg38.150200.bed.split1760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17600 0 1 2 100 hg38.150200.bed.split17600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17601 0 1 2 100 hg38.150200.bed.split17601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17602 0 1 2 100 hg38.150200.bed.split17602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17603 0 1 2 100 hg38.150200.bed.split17603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17604 0 1 2 100 hg38.150200.bed.split17604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17605 0 1 2 100 hg38.150200.bed.split17605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17606 0 1 2 100 hg38.150200.bed.split17606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17607 0 1 2 100 hg38.150200.bed.split17607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17608 0 1 2 100 hg38.150200.bed.split17608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17609 0 1 2 100 hg38.150200.bed.split17609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1761 0 1 2 100 hg38.150200.bed.split1761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17610 0 1 2 100 hg38.150200.bed.split17610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17611 0 1 2 100 hg38.150200.bed.split17611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17612 0 1 2 100 hg38.150200.bed.split17612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17613 0 1 2 100 hg38.150200.bed.split17613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17614 0 1 2 100 hg38.150200.bed.split17614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17615 0 1 2 100 hg38.150200.bed.split17615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17616 0 1 2 100 hg38.150200.bed.split17616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17617 0 1 2 100 hg38.150200.bed.split17617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17618 0 1 2 100 hg38.150200.bed.split17618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17619 0 1 2 100 hg38.150200.bed.split17619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1762 0 1 2 100 hg38.150200.bed.split1762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17620 0 1 2 100 hg38.150200.bed.split17620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17621 0 1 2 100 hg38.150200.bed.split17621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17622 0 1 2 100 hg38.150200.bed.split17622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17623 0 1 2 100 hg38.150200.bed.split17623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17624 0 1 2 100 hg38.150200.bed.split17624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17625 0 1 2 100 hg38.150200.bed.split17625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17626 0 1 2 100 hg38.150200.bed.split17626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17627 0 1 2 100 hg38.150200.bed.split17627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17628 0 1 2 100 hg38.150200.bed.split17628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17629 0 1 2 100 hg38.150200.bed.split17629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1763 0 1 2 100 hg38.150200.bed.split1763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17630 0 1 2 100 hg38.150200.bed.split17630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17631 0 1 2 100 hg38.150200.bed.split17631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17632 0 1 2 100 hg38.150200.bed.split17632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17633 0 1 2 100 hg38.150200.bed.split17633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17634 0 1 2 100 hg38.150200.bed.split17634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17635 0 1 2 100 hg38.150200.bed.split17635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17636 0 1 2 100 hg38.150200.bed.split17636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17637 0 1 2 100 hg38.150200.bed.split17637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17638 0 1 2 100 hg38.150200.bed.split17638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17639 0 1 2 100 hg38.150200.bed.split17639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1764 0 1 2 100 hg38.150200.bed.split1764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17640 0 1 2 100 hg38.150200.bed.split17640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17641 0 1 2 100 hg38.150200.bed.split17641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17642 0 1 2 100 hg38.150200.bed.split17642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17643 0 1 2 100 hg38.150200.bed.split17643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17644 0 1 2 100 hg38.150200.bed.split17644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17645 0 1 2 100 hg38.150200.bed.split17645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17646 0 1 2 100 hg38.150200.bed.split17646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17647 0 1 2 100 hg38.150200.bed.split17647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17648 0 1 2 100 hg38.150200.bed.split17648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17649 0 1 2 100 hg38.150200.bed.split17649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1765 0 1 2 100 hg38.150200.bed.split1765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17650 0 1 2 100 hg38.150200.bed.split17650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17651 0 1 2 100 hg38.150200.bed.split17651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17652 0 1 2 100 hg38.150200.bed.split17652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17653 0 1 2 100 hg38.150200.bed.split17653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17654 0 1 2 100 hg38.150200.bed.split17654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17655 0 1 2 100 hg38.150200.bed.split17655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17656 0 1 2 100 hg38.150200.bed.split17656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17657 0 1 2 100 hg38.150200.bed.split17657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17658 0 1 2 100 hg38.150200.bed.split17658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17659 0 1 2 100 hg38.150200.bed.split17659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1766 0 1 2 100 hg38.150200.bed.split1766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17660 0 1 2 100 hg38.150200.bed.split17660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17661 0 1 2 100 hg38.150200.bed.split17661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17662 0 1 2 100 hg38.150200.bed.split17662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17663 0 1 2 100 hg38.150200.bed.split17663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17664 0 1 2 100 hg38.150200.bed.split17664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17665 0 1 2 100 hg38.150200.bed.split17665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17666 0 1 2 100 hg38.150200.bed.split17666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17667 0 1 2 100 hg38.150200.bed.split17667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17668 0 1 2 100 hg38.150200.bed.split17668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17669 0 1 2 100 hg38.150200.bed.split17669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1767 0 1 2 100 hg38.150200.bed.split1767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17670 0 1 2 100 hg38.150200.bed.split17670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17671 0 1 2 100 hg38.150200.bed.split17671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17672 0 1 2 100 hg38.150200.bed.split17672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17673 0 1 2 100 hg38.150200.bed.split17673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17674 0 1 2 100 hg38.150200.bed.split17674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17675 0 1 2 100 hg38.150200.bed.split17675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17676 0 1 2 100 hg38.150200.bed.split17676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17677 0 1 2 100 hg38.150200.bed.split17677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17678 0 1 2 100 hg38.150200.bed.split17678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17679 0 1 2 100 hg38.150200.bed.split17679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1768 0 1 2 100 hg38.150200.bed.split1768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17680 0 1 2 100 hg38.150200.bed.split17680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17681 0 1 2 100 hg38.150200.bed.split17681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17682 0 1 2 100 hg38.150200.bed.split17682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17683 0 1 2 100 hg38.150200.bed.split17683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17684 0 1 2 100 hg38.150200.bed.split17684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17685 0 1 2 100 hg38.150200.bed.split17685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17686 0 1 2 100 hg38.150200.bed.split17686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17687 0 1 2 100 hg38.150200.bed.split17687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17688 0 1 2 100 hg38.150200.bed.split17688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17689 0 1 2 100 hg38.150200.bed.split17689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1769 0 1 2 100 hg38.150200.bed.split1769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17690 0 1 2 100 hg38.150200.bed.split17690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17691 0 1 2 100 hg38.150200.bed.split17691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17692 0 1 2 100 hg38.150200.bed.split17692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17693 0 1 2 100 hg38.150200.bed.split17693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17694 0 1 2 100 hg38.150200.bed.split17694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17695 0 1 2 100 hg38.150200.bed.split17695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17696 0 1 2 100 hg38.150200.bed.split17696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17697 0 1 2 100 hg38.150200.bed.split17697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17698 0 1 2 100 hg38.150200.bed.split17698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17699 0 1 2 100 hg38.150200.bed.split17699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split177 0 1 2 100 hg38.150200.bed.split177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1770 0 1 2 100 hg38.150200.bed.split1770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17700 0 1 2 100 hg38.150200.bed.split17700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17701 0 1 2 100 hg38.150200.bed.split17701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17702 0 1 2 100 hg38.150200.bed.split17702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17703 0 1 2 100 hg38.150200.bed.split17703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17704 0 1 2 100 hg38.150200.bed.split17704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17705 0 1 2 100 hg38.150200.bed.split17705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17706 0 1 2 100 hg38.150200.bed.split17706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17707 0 1 2 100 hg38.150200.bed.split17707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17708 0 1 2 100 hg38.150200.bed.split17708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17709 0 1 2 100 hg38.150200.bed.split17709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1771 0 1 2 100 hg38.150200.bed.split1771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17710 0 1 2 100 hg38.150200.bed.split17710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17711 0 1 2 100 hg38.150200.bed.split17711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17712 0 1 2 100 hg38.150200.bed.split17712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17713 0 1 2 100 hg38.150200.bed.split17713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17714 0 1 2 100 hg38.150200.bed.split17714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17715 0 1 2 100 hg38.150200.bed.split17715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17716 0 1 2 100 hg38.150200.bed.split17716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17717 0 1 2 100 hg38.150200.bed.split17717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17718 0 1 2 100 hg38.150200.bed.split17718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17719 0 1 2 100 hg38.150200.bed.split17719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1772 0 1 2 100 hg38.150200.bed.split1772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17720 0 1 2 100 hg38.150200.bed.split17720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17721 0 1 2 100 hg38.150200.bed.split17721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17722 0 1 2 100 hg38.150200.bed.split17722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17723 0 1 2 100 hg38.150200.bed.split17723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17724 0 1 2 100 hg38.150200.bed.split17724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17725 0 1 2 100 hg38.150200.bed.split17725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17726 0 1 2 100 hg38.150200.bed.split17726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17727 0 1 2 100 hg38.150200.bed.split17727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17728 0 1 2 100 hg38.150200.bed.split17728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17729 0 1 2 100 hg38.150200.bed.split17729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1773 0 1 2 100 hg38.150200.bed.split1773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17730 0 1 2 100 hg38.150200.bed.split17730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17731 0 1 2 100 hg38.150200.bed.split17731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17732 0 1 2 100 hg38.150200.bed.split17732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17733 0 1 2 100 hg38.150200.bed.split17733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17734 0 1 2 100 hg38.150200.bed.split17734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17735 0 1 2 100 hg38.150200.bed.split17735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17736 0 1 2 100 hg38.150200.bed.split17736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17737 0 1 2 100 hg38.150200.bed.split17737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17738 0 1 2 100 hg38.150200.bed.split17738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17739 0 1 2 100 hg38.150200.bed.split17739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1774 0 1 2 100 hg38.150200.bed.split1774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17740 0 1 2 100 hg38.150200.bed.split17740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17741 0 1 2 100 hg38.150200.bed.split17741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17742 0 1 2 100 hg38.150200.bed.split17742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17743 0 1 2 100 hg38.150200.bed.split17743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17744 0 1 2 100 hg38.150200.bed.split17744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17745 0 1 2 100 hg38.150200.bed.split17745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17746 0 1 2 100 hg38.150200.bed.split17746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17747 0 1 2 100 hg38.150200.bed.split17747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17748 0 1 2 100 hg38.150200.bed.split17748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17749 0 1 2 100 hg38.150200.bed.split17749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1775 0 1 2 100 hg38.150200.bed.split1775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17750 0 1 2 100 hg38.150200.bed.split17750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17751 0 1 2 100 hg38.150200.bed.split17751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17752 0 1 2 100 hg38.150200.bed.split17752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17753 0 1 2 100 hg38.150200.bed.split17753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17754 0 1 2 100 hg38.150200.bed.split17754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17755 0 1 2 100 hg38.150200.bed.split17755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17756 0 1 2 100 hg38.150200.bed.split17756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17757 0 1 2 100 hg38.150200.bed.split17757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17758 0 1 2 100 hg38.150200.bed.split17758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17759 0 1 2 100 hg38.150200.bed.split17759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1776 0 1 2 100 hg38.150200.bed.split1776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17760 0 1 2 100 hg38.150200.bed.split17760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17761 0 1 2 100 hg38.150200.bed.split17761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17762 0 1 2 100 hg38.150200.bed.split17762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17763 0 1 2 100 hg38.150200.bed.split17763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17764 0 1 2 100 hg38.150200.bed.split17764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17765 0 1 2 100 hg38.150200.bed.split17765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17766 0 1 2 100 hg38.150200.bed.split17766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17767 0 1 2 100 hg38.150200.bed.split17767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17768 0 1 2 100 hg38.150200.bed.split17768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17769 0 1 2 100 hg38.150200.bed.split17769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1777 0 1 2 100 hg38.150200.bed.split1777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17770 0 1 2 100 hg38.150200.bed.split17770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17771 0 1 2 100 hg38.150200.bed.split17771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17772 0 1 2 100 hg38.150200.bed.split17772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17773 0 1 2 100 hg38.150200.bed.split17773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17774 0 1 2 100 hg38.150200.bed.split17774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17775 0 1 2 100 hg38.150200.bed.split17775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17776 0 1 2 100 hg38.150200.bed.split17776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17777 0 1 2 100 hg38.150200.bed.split17777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17778 0 1 2 100 hg38.150200.bed.split17778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17779 0 1 2 100 hg38.150200.bed.split17779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1778 0 1 2 100 hg38.150200.bed.split1778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17780 0 1 2 100 hg38.150200.bed.split17780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17781 0 1 2 100 hg38.150200.bed.split17781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17782 0 1 2 100 hg38.150200.bed.split17782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17783 0 1 2 100 hg38.150200.bed.split17783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17784 0 1 2 100 hg38.150200.bed.split17784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17785 0 1 2 100 hg38.150200.bed.split17785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17786 0 1 2 100 hg38.150200.bed.split17786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17787 0 1 2 100 hg38.150200.bed.split17787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17788 0 1 2 100 hg38.150200.bed.split17788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17789 0 1 2 100 hg38.150200.bed.split17789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1779 0 1 2 100 hg38.150200.bed.split1779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17790 0 1 2 100 hg38.150200.bed.split17790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17791 0 1 2 100 hg38.150200.bed.split17791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17792 0 1 2 100 hg38.150200.bed.split17792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17793 0 1 2 100 hg38.150200.bed.split17793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17794 0 1 2 100 hg38.150200.bed.split17794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17795 0 1 2 100 hg38.150200.bed.split17795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17796 0 1 2 100 hg38.150200.bed.split17796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17797 0 1 2 100 hg38.150200.bed.split17797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17798 0 1 2 100 hg38.150200.bed.split17798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17799 0 1 2 100 hg38.150200.bed.split17799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split178 0 1 2 100 hg38.150200.bed.split178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1780 0 1 2 100 hg38.150200.bed.split1780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17800 0 1 2 100 hg38.150200.bed.split17800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17801 0 1 2 100 hg38.150200.bed.split17801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17802 0 1 2 100 hg38.150200.bed.split17802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17803 0 1 2 100 hg38.150200.bed.split17803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17804 0 1 2 100 hg38.150200.bed.split17804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17805 0 1 2 100 hg38.150200.bed.split17805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17806 0 1 2 100 hg38.150200.bed.split17806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17807 0 1 2 100 hg38.150200.bed.split17807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17808 0 1 2 100 hg38.150200.bed.split17808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17809 0 1 2 100 hg38.150200.bed.split17809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1781 0 1 2 100 hg38.150200.bed.split1781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17810 0 1 2 100 hg38.150200.bed.split17810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17811 0 1 2 100 hg38.150200.bed.split17811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17812 0 1 2 100 hg38.150200.bed.split17812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17813 0 1 2 100 hg38.150200.bed.split17813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17814 0 1 2 100 hg38.150200.bed.split17814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17815 0 1 2 100 hg38.150200.bed.split17815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17816 0 1 2 100 hg38.150200.bed.split17816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17817 0 1 2 100 hg38.150200.bed.split17817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17818 0 1 2 100 hg38.150200.bed.split17818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17819 0 1 2 100 hg38.150200.bed.split17819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1782 0 1 2 100 hg38.150200.bed.split1782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17820 0 1 2 100 hg38.150200.bed.split17820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17821 0 1 2 100 hg38.150200.bed.split17821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17822 0 1 2 100 hg38.150200.bed.split17822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17823 0 1 2 100 hg38.150200.bed.split17823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17824 0 1 2 100 hg38.150200.bed.split17824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17825 0 1 2 100 hg38.150200.bed.split17825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17826 0 1 2 100 hg38.150200.bed.split17826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17827 0 1 2 100 hg38.150200.bed.split17827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17828 0 1 2 100 hg38.150200.bed.split17828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17829 0 1 2 100 hg38.150200.bed.split17829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1783 0 1 2 100 hg38.150200.bed.split1783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17830 0 1 2 100 hg38.150200.bed.split17830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17831 0 1 2 100 hg38.150200.bed.split17831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17832 0 1 2 100 hg38.150200.bed.split17832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17833 0 1 2 100 hg38.150200.bed.split17833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17834 0 1 2 100 hg38.150200.bed.split17834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17835 0 1 2 100 hg38.150200.bed.split17835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17836 0 1 2 100 hg38.150200.bed.split17836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17837 0 1 2 100 hg38.150200.bed.split17837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17838 0 1 2 100 hg38.150200.bed.split17838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17839 0 1 2 100 hg38.150200.bed.split17839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1784 0 1 2 100 hg38.150200.bed.split1784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17840 0 1 2 100 hg38.150200.bed.split17840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17841 0 1 2 100 hg38.150200.bed.split17841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17842 0 1 2 100 hg38.150200.bed.split17842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17843 0 1 2 100 hg38.150200.bed.split17843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17844 0 1 2 100 hg38.150200.bed.split17844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17845 0 1 2 100 hg38.150200.bed.split17845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17846 0 1 2 100 hg38.150200.bed.split17846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17847 0 1 2 100 hg38.150200.bed.split17847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17848 0 1 2 100 hg38.150200.bed.split17848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17849 0 1 2 100 hg38.150200.bed.split17849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1785 0 1 2 100 hg38.150200.bed.split1785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17850 0 1 2 100 hg38.150200.bed.split17850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17851 0 1 2 100 hg38.150200.bed.split17851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17852 0 1 2 100 hg38.150200.bed.split17852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17853 0 1 2 100 hg38.150200.bed.split17853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17854 0 1 2 100 hg38.150200.bed.split17854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17855 0 1 2 100 hg38.150200.bed.split17855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17856 0 1 2 100 hg38.150200.bed.split17856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17857 0 1 2 100 hg38.150200.bed.split17857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17858 0 1 2 100 hg38.150200.bed.split17858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17859 0 1 2 100 hg38.150200.bed.split17859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1786 0 1 2 100 hg38.150200.bed.split1786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17860 0 1 2 100 hg38.150200.bed.split17860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17861 0 1 2 100 hg38.150200.bed.split17861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17862 0 1 2 100 hg38.150200.bed.split17862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17863 0 1 2 100 hg38.150200.bed.split17863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17864 0 1 2 100 hg38.150200.bed.split17864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17865 0 1 2 100 hg38.150200.bed.split17865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17866 0 1 2 100 hg38.150200.bed.split17866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17867 0 1 2 100 hg38.150200.bed.split17867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17868 0 1 2 100 hg38.150200.bed.split17868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17869 0 1 2 100 hg38.150200.bed.split17869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1787 0 1 2 100 hg38.150200.bed.split1787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17870 0 1 2 100 hg38.150200.bed.split17870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17871 0 1 2 100 hg38.150200.bed.split17871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17872 0 1 2 100 hg38.150200.bed.split17872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17873 0 1 2 100 hg38.150200.bed.split17873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17874 0 1 2 100 hg38.150200.bed.split17874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17875 0 1 2 100 hg38.150200.bed.split17875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17876 0 1 2 100 hg38.150200.bed.split17876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17877 0 1 2 100 hg38.150200.bed.split17877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17878 0 1 2 100 hg38.150200.bed.split17878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17879 0 1 2 100 hg38.150200.bed.split17879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1788 0 1 2 100 hg38.150200.bed.split1788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17880 0 1 2 100 hg38.150200.bed.split17880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17881 0 1 2 100 hg38.150200.bed.split17881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17882 0 1 2 100 hg38.150200.bed.split17882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17883 0 1 2 100 hg38.150200.bed.split17883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17884 0 1 2 100 hg38.150200.bed.split17884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17885 0 1 2 100 hg38.150200.bed.split17885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17886 0 1 2 100 hg38.150200.bed.split17886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17887 0 1 2 100 hg38.150200.bed.split17887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17888 0 1 2 100 hg38.150200.bed.split17888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17889 0 1 2 100 hg38.150200.bed.split17889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1789 0 1 2 100 hg38.150200.bed.split1789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17890 0 1 2 100 hg38.150200.bed.split17890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17891 0 1 2 100 hg38.150200.bed.split17891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17892 0 1 2 100 hg38.150200.bed.split17892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17893 0 1 2 100 hg38.150200.bed.split17893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17894 0 1 2 100 hg38.150200.bed.split17894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17895 0 1 2 100 hg38.150200.bed.split17895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17896 0 1 2 100 hg38.150200.bed.split17896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17897 0 1 2 100 hg38.150200.bed.split17897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17898 0 1 2 100 hg38.150200.bed.split17898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17899 0 1 2 100 hg38.150200.bed.split17899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split179 0 1 2 100 hg38.150200.bed.split179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1790 0 1 2 100 hg38.150200.bed.split1790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17900 0 1 2 100 hg38.150200.bed.split17900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17901 0 1 2 100 hg38.150200.bed.split17901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17902 0 1 2 100 hg38.150200.bed.split17902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17903 0 1 2 100 hg38.150200.bed.split17903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17904 0 1 2 100 hg38.150200.bed.split17904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17905 0 1 2 100 hg38.150200.bed.split17905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17906 0 1 2 100 hg38.150200.bed.split17906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17907 0 1 2 100 hg38.150200.bed.split17907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17908 0 1 2 100 hg38.150200.bed.split17908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17909 0 1 2 100 hg38.150200.bed.split17909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1791 0 1 2 100 hg38.150200.bed.split1791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17910 0 1 2 100 hg38.150200.bed.split17910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17911 0 1 2 100 hg38.150200.bed.split17911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17912 0 1 2 100 hg38.150200.bed.split17912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17913 0 1 2 100 hg38.150200.bed.split17913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17914 0 1 2 100 hg38.150200.bed.split17914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17915 0 1 2 100 hg38.150200.bed.split17915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17916 0 1 2 100 hg38.150200.bed.split17916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17917 0 1 2 100 hg38.150200.bed.split17917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17918 0 1 2 100 hg38.150200.bed.split17918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17919 0 1 2 100 hg38.150200.bed.split17919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1792 0 1 2 100 hg38.150200.bed.split1792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17920 0 1 2 100 hg38.150200.bed.split17920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17921 0 1 2 100 hg38.150200.bed.split17921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17922 0 1 2 100 hg38.150200.bed.split17922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17923 0 1 2 100 hg38.150200.bed.split17923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17924 0 1 2 100 hg38.150200.bed.split17924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17925 0 1 2 100 hg38.150200.bed.split17925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17926 0 1 2 100 hg38.150200.bed.split17926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17927 0 1 2 100 hg38.150200.bed.split17927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17928 0 1 2 100 hg38.150200.bed.split17928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17929 0 1 2 100 hg38.150200.bed.split17929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1793 0 1 2 100 hg38.150200.bed.split1793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17930 0 1 2 100 hg38.150200.bed.split17930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17931 0 1 2 100 hg38.150200.bed.split17931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17932 0 1 2 100 hg38.150200.bed.split17932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17933 0 1 2 100 hg38.150200.bed.split17933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17934 0 1 2 100 hg38.150200.bed.split17934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17935 0 1 2 100 hg38.150200.bed.split17935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17936 0 1 2 100 hg38.150200.bed.split17936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17937 0 1 2 100 hg38.150200.bed.split17937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17938 0 1 2 100 hg38.150200.bed.split17938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17939 0 1 2 100 hg38.150200.bed.split17939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1794 0 1 2 100 hg38.150200.bed.split1794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17940 0 1 2 100 hg38.150200.bed.split17940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17941 0 1 2 100 hg38.150200.bed.split17941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17942 0 1 2 100 hg38.150200.bed.split17942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17943 0 1 2 100 hg38.150200.bed.split17943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17944 0 1 2 100 hg38.150200.bed.split17944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17945 0 1 2 100 hg38.150200.bed.split17945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17946 0 1 2 100 hg38.150200.bed.split17946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17947 0 1 2 100 hg38.150200.bed.split17947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17948 0 1 2 100 hg38.150200.bed.split17948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17949 0 1 2 100 hg38.150200.bed.split17949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1795 0 1 2 100 hg38.150200.bed.split1795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17950 0 1 2 100 hg38.150200.bed.split17950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17951 0 1 2 100 hg38.150200.bed.split17951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17952 0 1 2 100 hg38.150200.bed.split17952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17953 0 1 2 100 hg38.150200.bed.split17953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17954 0 1 2 100 hg38.150200.bed.split17954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17955 0 1 2 100 hg38.150200.bed.split17955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17956 0 1 2 100 hg38.150200.bed.split17956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17957 0 1 2 100 hg38.150200.bed.split17957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17958 0 1 2 100 hg38.150200.bed.split17958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17959 0 1 2 100 hg38.150200.bed.split17959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1796 0 1 2 100 hg38.150200.bed.split1796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17960 0 1 2 100 hg38.150200.bed.split17960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17961 0 1 2 100 hg38.150200.bed.split17961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17962 0 1 2 100 hg38.150200.bed.split17962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17963 0 1 2 100 hg38.150200.bed.split17963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17964 0 1 2 100 hg38.150200.bed.split17964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17965 0 1 2 100 hg38.150200.bed.split17965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17966 0 1 2 100 hg38.150200.bed.split17966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17967 0 1 2 100 hg38.150200.bed.split17967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17968 0 1 2 100 hg38.150200.bed.split17968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17969 0 1 2 100 hg38.150200.bed.split17969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1797 0 1 2 100 hg38.150200.bed.split1797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17970 0 1 2 100 hg38.150200.bed.split17970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17971 0 1 2 100 hg38.150200.bed.split17971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17972 0 1 2 100 hg38.150200.bed.split17972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17973 0 1 2 100 hg38.150200.bed.split17973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17974 0 1 2 100 hg38.150200.bed.split17974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17975 0 1 2 100 hg38.150200.bed.split17975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17976 0 1 2 100 hg38.150200.bed.split17976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17977 0 1 2 100 hg38.150200.bed.split17977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17978 0 1 2 100 hg38.150200.bed.split17978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17979 0 1 2 100 hg38.150200.bed.split17979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1798 0 1 2 100 hg38.150200.bed.split1798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17980 0 1 2 100 hg38.150200.bed.split17980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17981 0 1 2 100 hg38.150200.bed.split17981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17982 0 1 2 100 hg38.150200.bed.split17982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17983 0 1 2 100 hg38.150200.bed.split17983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17984 0 1 2 100 hg38.150200.bed.split17984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17985 0 1 2 100 hg38.150200.bed.split17985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17986 0 1 2 100 hg38.150200.bed.split17986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17987 0 1 2 100 hg38.150200.bed.split17987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17988 0 1 2 100 hg38.150200.bed.split17988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17989 0 1 2 100 hg38.150200.bed.split17989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1799 0 1 2 100 hg38.150200.bed.split1799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17990 0 1 2 100 hg38.150200.bed.split17990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17991 0 1 2 100 hg38.150200.bed.split17991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17992 0 1 2 100 hg38.150200.bed.split17992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17993 0 1 2 100 hg38.150200.bed.split17993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17994 0 1 2 100 hg38.150200.bed.split17994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17995 0 1 2 100 hg38.150200.bed.split17995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17996 0 1 2 100 hg38.150200.bed.split17996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17997 0 1 2 100 hg38.150200.bed.split17997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17998 0 1 2 100 hg38.150200.bed.split17998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split17999 0 1 2 100 hg38.150200.bed.split17999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18 0 1 2 100 hg38.150200.bed.split18.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split180 0 1 2 100 hg38.150200.bed.split180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1800 0 1 2 100 hg38.150200.bed.split1800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18000 0 1 2 100 hg38.150200.bed.split18000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18001 0 1 2 100 hg38.150200.bed.split18001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18002 0 1 2 100 hg38.150200.bed.split18002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18003 0 1 2 100 hg38.150200.bed.split18003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18004 0 1 2 100 hg38.150200.bed.split18004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18005 0 1 2 100 hg38.150200.bed.split18005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18006 0 1 2 100 hg38.150200.bed.split18006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18007 0 1 2 100 hg38.150200.bed.split18007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18008 0 1 2 100 hg38.150200.bed.split18008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18009 0 1 2 100 hg38.150200.bed.split18009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1801 0 1 2 100 hg38.150200.bed.split1801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18010 0 1 2 100 hg38.150200.bed.split18010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18011 0 1 2 100 hg38.150200.bed.split18011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18012 0 1 2 100 hg38.150200.bed.split18012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18013 0 1 2 100 hg38.150200.bed.split18013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18014 0 1 2 100 hg38.150200.bed.split18014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18015 0 1 2 100 hg38.150200.bed.split18015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18016 0 1 2 100 hg38.150200.bed.split18016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18017 0 1 2 100 hg38.150200.bed.split18017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18018 0 1 2 100 hg38.150200.bed.split18018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18019 0 1 2 100 hg38.150200.bed.split18019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1802 0 1 2 100 hg38.150200.bed.split1802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18020 0 1 2 100 hg38.150200.bed.split18020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18021 0 1 2 100 hg38.150200.bed.split18021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18022 0 1 2 100 hg38.150200.bed.split18022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18023 0 1 2 100 hg38.150200.bed.split18023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18024 0 1 2 100 hg38.150200.bed.split18024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18025 0 1 2 100 hg38.150200.bed.split18025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18026 0 1 2 100 hg38.150200.bed.split18026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18027 0 1 2 100 hg38.150200.bed.split18027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18028 0 1 2 100 hg38.150200.bed.split18028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18029 0 1 2 100 hg38.150200.bed.split18029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1803 0 1 2 100 hg38.150200.bed.split1803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18030 0 1 2 100 hg38.150200.bed.split18030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18031 0 1 2 100 hg38.150200.bed.split18031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18032 0 1 2 100 hg38.150200.bed.split18032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18033 0 1 2 100 hg38.150200.bed.split18033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18034 0 1 2 100 hg38.150200.bed.split18034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18035 0 1 2 100 hg38.150200.bed.split18035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18036 0 1 2 100 hg38.150200.bed.split18036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18037 0 1 2 100 hg38.150200.bed.split18037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18038 0 1 2 100 hg38.150200.bed.split18038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18039 0 1 2 100 hg38.150200.bed.split18039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1804 0 1 2 100 hg38.150200.bed.split1804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18040 0 1 2 100 hg38.150200.bed.split18040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18041 0 1 2 100 hg38.150200.bed.split18041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18042 0 1 2 100 hg38.150200.bed.split18042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18043 0 1 2 100 hg38.150200.bed.split18043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18044 0 1 2 100 hg38.150200.bed.split18044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18045 0 1 2 100 hg38.150200.bed.split18045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18046 0 1 2 100 hg38.150200.bed.split18046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18047 0 1 2 100 hg38.150200.bed.split18047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18048 0 1 2 100 hg38.150200.bed.split18048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18049 0 1 2 100 hg38.150200.bed.split18049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1805 0 1 2 100 hg38.150200.bed.split1805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18050 0 1 2 100 hg38.150200.bed.split18050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18051 0 1 2 100 hg38.150200.bed.split18051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18052 0 1 2 100 hg38.150200.bed.split18052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18053 0 1 2 100 hg38.150200.bed.split18053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18054 0 1 2 100 hg38.150200.bed.split18054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18055 0 1 2 100 hg38.150200.bed.split18055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18056 0 1 2 100 hg38.150200.bed.split18056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18057 0 1 2 100 hg38.150200.bed.split18057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18058 0 1 2 100 hg38.150200.bed.split18058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18059 0 1 2 100 hg38.150200.bed.split18059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1806 0 1 2 100 hg38.150200.bed.split1806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18060 0 1 2 100 hg38.150200.bed.split18060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18061 0 1 2 100 hg38.150200.bed.split18061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18062 0 1 2 100 hg38.150200.bed.split18062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18063 0 1 2 100 hg38.150200.bed.split18063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18064 0 1 2 100 hg38.150200.bed.split18064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18065 0 1 2 100 hg38.150200.bed.split18065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18066 0 1 2 100 hg38.150200.bed.split18066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18067 0 1 2 100 hg38.150200.bed.split18067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18068 0 1 2 100 hg38.150200.bed.split18068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18069 0 1 2 100 hg38.150200.bed.split18069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1807 0 1 2 100 hg38.150200.bed.split1807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18070 0 1 2 100 hg38.150200.bed.split18070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18071 0 1 2 100 hg38.150200.bed.split18071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18072 0 1 2 100 hg38.150200.bed.split18072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18073 0 1 2 100 hg38.150200.bed.split18073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18074 0 1 2 100 hg38.150200.bed.split18074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18075 0 1 2 100 hg38.150200.bed.split18075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18076 0 1 2 100 hg38.150200.bed.split18076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18077 0 1 2 100 hg38.150200.bed.split18077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18078 0 1 2 100 hg38.150200.bed.split18078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18079 0 1 2 100 hg38.150200.bed.split18079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1808 0 1 2 100 hg38.150200.bed.split1808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18080 0 1 2 100 hg38.150200.bed.split18080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18081 0 1 2 100 hg38.150200.bed.split18081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18082 0 1 2 100 hg38.150200.bed.split18082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18083 0 1 2 100 hg38.150200.bed.split18083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18084 0 1 2 100 hg38.150200.bed.split18084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18085 0 1 2 100 hg38.150200.bed.split18085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18086 0 1 2 100 hg38.150200.bed.split18086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18087 0 1 2 100 hg38.150200.bed.split18087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18088 0 1 2 100 hg38.150200.bed.split18088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18089 0 1 2 100 hg38.150200.bed.split18089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1809 0 1 2 100 hg38.150200.bed.split1809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18090 0 1 2 100 hg38.150200.bed.split18090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18091 0 1 2 100 hg38.150200.bed.split18091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18092 0 1 2 100 hg38.150200.bed.split18092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18093 0 1 2 100 hg38.150200.bed.split18093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18094 0 1 2 100 hg38.150200.bed.split18094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18095 0 1 2 100 hg38.150200.bed.split18095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18096 0 1 2 100 hg38.150200.bed.split18096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18097 0 1 2 100 hg38.150200.bed.split18097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18098 0 1 2 100 hg38.150200.bed.split18098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18099 0 1 2 100 hg38.150200.bed.split18099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split181 0 1 2 100 hg38.150200.bed.split181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1810 0 1 2 100 hg38.150200.bed.split1810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18100 0 1 2 100 hg38.150200.bed.split18100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18101 0 1 2 100 hg38.150200.bed.split18101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18102 0 1 2 100 hg38.150200.bed.split18102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18103 0 1 2 100 hg38.150200.bed.split18103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18104 0 1 2 100 hg38.150200.bed.split18104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18105 0 1 2 100 hg38.150200.bed.split18105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18106 0 1 2 100 hg38.150200.bed.split18106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18107 0 1 2 100 hg38.150200.bed.split18107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18108 0 1 2 100 hg38.150200.bed.split18108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18109 0 1 2 100 hg38.150200.bed.split18109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1811 0 1 2 100 hg38.150200.bed.split1811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18110 0 1 2 100 hg38.150200.bed.split18110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18111 0 1 2 100 hg38.150200.bed.split18111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18112 0 1 2 100 hg38.150200.bed.split18112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18113 0 1 2 100 hg38.150200.bed.split18113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18114 0 1 2 100 hg38.150200.bed.split18114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18115 0 1 2 100 hg38.150200.bed.split18115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18116 0 1 2 100 hg38.150200.bed.split18116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18117 0 1 2 100 hg38.150200.bed.split18117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18118 0 1 2 100 hg38.150200.bed.split18118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18119 0 1 2 100 hg38.150200.bed.split18119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1812 0 1 2 100 hg38.150200.bed.split1812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18120 0 1 2 100 hg38.150200.bed.split18120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18121 0 1 2 100 hg38.150200.bed.split18121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18122 0 1 2 100 hg38.150200.bed.split18122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18123 0 1 2 100 hg38.150200.bed.split18123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18124 0 1 2 100 hg38.150200.bed.split18124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18125 0 1 2 100 hg38.150200.bed.split18125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18126 0 1 2 100 hg38.150200.bed.split18126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18127 0 1 2 100 hg38.150200.bed.split18127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18128 0 1 2 100 hg38.150200.bed.split18128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18129 0 1 2 100 hg38.150200.bed.split18129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1813 0 1 2 100 hg38.150200.bed.split1813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18130 0 1 2 100 hg38.150200.bed.split18130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18131 0 1 2 100 hg38.150200.bed.split18131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18132 0 1 2 100 hg38.150200.bed.split18132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18133 0 1 2 100 hg38.150200.bed.split18133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18134 0 1 2 100 hg38.150200.bed.split18134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18135 0 1 2 100 hg38.150200.bed.split18135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18136 0 1 2 100 hg38.150200.bed.split18136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18137 0 1 2 100 hg38.150200.bed.split18137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18138 0 1 2 100 hg38.150200.bed.split18138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18139 0 1 2 100 hg38.150200.bed.split18139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1814 0 1 2 100 hg38.150200.bed.split1814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18140 0 1 2 100 hg38.150200.bed.split18140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18141 0 1 2 100 hg38.150200.bed.split18141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18142 0 1 2 100 hg38.150200.bed.split18142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18143 0 1 2 100 hg38.150200.bed.split18143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18144 0 1 2 100 hg38.150200.bed.split18144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18145 0 1 2 100 hg38.150200.bed.split18145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18146 0 1 2 100 hg38.150200.bed.split18146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18147 0 1 2 100 hg38.150200.bed.split18147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18148 0 1 2 100 hg38.150200.bed.split18148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18149 0 1 2 100 hg38.150200.bed.split18149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1815 0 1 2 100 hg38.150200.bed.split1815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18150 0 1 2 100 hg38.150200.bed.split18150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18151 0 1 2 100 hg38.150200.bed.split18151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18152 0 1 2 100 hg38.150200.bed.split18152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18153 0 1 2 100 hg38.150200.bed.split18153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18154 0 1 2 100 hg38.150200.bed.split18154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18155 0 1 2 100 hg38.150200.bed.split18155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18156 0 1 2 100 hg38.150200.bed.split18156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18157 0 1 2 100 hg38.150200.bed.split18157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18158 0 1 2 100 hg38.150200.bed.split18158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18159 0 1 2 100 hg38.150200.bed.split18159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1816 0 1 2 100 hg38.150200.bed.split1816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18160 0 1 2 100 hg38.150200.bed.split18160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18161 0 1 2 100 hg38.150200.bed.split18161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18162 0 1 2 100 hg38.150200.bed.split18162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18163 0 1 2 100 hg38.150200.bed.split18163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18164 0 1 2 100 hg38.150200.bed.split18164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18165 0 1 2 100 hg38.150200.bed.split18165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18166 0 1 2 100 hg38.150200.bed.split18166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18167 0 1 2 100 hg38.150200.bed.split18167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18168 0 1 2 100 hg38.150200.bed.split18168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18169 0 1 2 100 hg38.150200.bed.split18169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1817 0 1 2 100 hg38.150200.bed.split1817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18170 0 1 2 100 hg38.150200.bed.split18170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18171 0 1 2 100 hg38.150200.bed.split18171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18172 0 1 2 100 hg38.150200.bed.split18172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18173 0 1 2 100 hg38.150200.bed.split18173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18174 0 1 2 100 hg38.150200.bed.split18174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18175 0 1 2 100 hg38.150200.bed.split18175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18176 0 1 2 100 hg38.150200.bed.split18176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18177 0 1 2 100 hg38.150200.bed.split18177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18178 0 1 2 100 hg38.150200.bed.split18178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18179 0 1 2 100 hg38.150200.bed.split18179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1818 0 1 2 100 hg38.150200.bed.split1818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18180 0 1 2 100 hg38.150200.bed.split18180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18181 0 1 2 100 hg38.150200.bed.split18181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18182 0 1 2 100 hg38.150200.bed.split18182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18183 0 1 2 100 hg38.150200.bed.split18183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18184 0 1 2 100 hg38.150200.bed.split18184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18185 0 1 2 100 hg38.150200.bed.split18185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18186 0 1 2 100 hg38.150200.bed.split18186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18187 0 1 2 100 hg38.150200.bed.split18187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18188 0 1 2 100 hg38.150200.bed.split18188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18189 0 1 2 100 hg38.150200.bed.split18189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1819 0 1 2 100 hg38.150200.bed.split1819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18190 0 1 2 100 hg38.150200.bed.split18190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18191 0 1 2 100 hg38.150200.bed.split18191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18192 0 1 2 100 hg38.150200.bed.split18192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18193 0 1 2 100 hg38.150200.bed.split18193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18194 0 1 2 100 hg38.150200.bed.split18194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18195 0 1 2 100 hg38.150200.bed.split18195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18196 0 1 2 100 hg38.150200.bed.split18196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18197 0 1 2 100 hg38.150200.bed.split18197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18198 0 1 2 100 hg38.150200.bed.split18198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18199 0 1 2 100 hg38.150200.bed.split18199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split182 0 1 2 100 hg38.150200.bed.split182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1820 0 1 2 100 hg38.150200.bed.split1820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18200 0 1 2 100 hg38.150200.bed.split18200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18201 0 1 2 100 hg38.150200.bed.split18201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18202 0 1 2 100 hg38.150200.bed.split18202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18203 0 1 2 100 hg38.150200.bed.split18203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18204 0 1 2 100 hg38.150200.bed.split18204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18205 0 1 2 100 hg38.150200.bed.split18205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18206 0 1 2 100 hg38.150200.bed.split18206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18207 0 1 2 100 hg38.150200.bed.split18207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18208 0 1 2 100 hg38.150200.bed.split18208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18209 0 1 2 100 hg38.150200.bed.split18209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1821 0 1 2 100 hg38.150200.bed.split1821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18210 0 1 2 100 hg38.150200.bed.split18210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18211 0 1 2 100 hg38.150200.bed.split18211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18212 0 1 2 100 hg38.150200.bed.split18212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18213 0 1 2 100 hg38.150200.bed.split18213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18214 0 1 2 100 hg38.150200.bed.split18214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18215 0 1 2 100 hg38.150200.bed.split18215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18216 0 1 2 100 hg38.150200.bed.split18216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18217 0 1 2 100 hg38.150200.bed.split18217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18218 0 1 2 100 hg38.150200.bed.split18218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18219 0 1 2 100 hg38.150200.bed.split18219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1822 0 1 2 100 hg38.150200.bed.split1822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18220 0 1 2 100 hg38.150200.bed.split18220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18221 0 1 2 100 hg38.150200.bed.split18221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18222 0 1 2 100 hg38.150200.bed.split18222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18223 0 1 2 100 hg38.150200.bed.split18223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18224 0 1 2 100 hg38.150200.bed.split18224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18225 0 1 2 100 hg38.150200.bed.split18225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18226 0 1 2 100 hg38.150200.bed.split18226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18227 0 1 2 100 hg38.150200.bed.split18227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18228 0 1 2 100 hg38.150200.bed.split18228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18229 0 1 2 100 hg38.150200.bed.split18229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1823 0 1 2 100 hg38.150200.bed.split1823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18230 0 1 2 100 hg38.150200.bed.split18230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18231 0 1 2 100 hg38.150200.bed.split18231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18232 0 1 2 100 hg38.150200.bed.split18232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18233 0 1 2 100 hg38.150200.bed.split18233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18234 0 1 2 100 hg38.150200.bed.split18234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18235 0 1 2 100 hg38.150200.bed.split18235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18236 0 1 2 100 hg38.150200.bed.split18236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18237 0 1 2 100 hg38.150200.bed.split18237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18238 0 1 2 100 hg38.150200.bed.split18238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18239 0 1 2 100 hg38.150200.bed.split18239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1824 0 1 2 100 hg38.150200.bed.split1824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18240 0 1 2 100 hg38.150200.bed.split18240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18241 0 1 2 100 hg38.150200.bed.split18241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18242 0 1 2 100 hg38.150200.bed.split18242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18243 0 1 2 100 hg38.150200.bed.split18243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18244 0 1 2 100 hg38.150200.bed.split18244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18245 0 1 2 100 hg38.150200.bed.split18245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18246 0 1 2 100 hg38.150200.bed.split18246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18247 0 1 2 100 hg38.150200.bed.split18247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18248 0 1 2 100 hg38.150200.bed.split18248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18249 0 1 2 100 hg38.150200.bed.split18249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1825 0 1 2 100 hg38.150200.bed.split1825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18250 0 1 2 100 hg38.150200.bed.split18250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18251 0 1 2 100 hg38.150200.bed.split18251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18252 0 1 2 100 hg38.150200.bed.split18252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18253 0 1 2 100 hg38.150200.bed.split18253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18254 0 1 2 100 hg38.150200.bed.split18254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18255 0 1 2 100 hg38.150200.bed.split18255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18256 0 1 2 100 hg38.150200.bed.split18256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18257 0 1 2 100 hg38.150200.bed.split18257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18258 0 1 2 100 hg38.150200.bed.split18258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18259 0 1 2 100 hg38.150200.bed.split18259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1826 0 1 2 100 hg38.150200.bed.split1826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18260 0 1 2 100 hg38.150200.bed.split18260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18261 0 1 2 100 hg38.150200.bed.split18261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18262 0 1 2 100 hg38.150200.bed.split18262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18263 0 1 2 100 hg38.150200.bed.split18263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18264 0 1 2 100 hg38.150200.bed.split18264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18265 0 1 2 100 hg38.150200.bed.split18265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18266 0 1 2 100 hg38.150200.bed.split18266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18267 0 1 2 100 hg38.150200.bed.split18267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18268 0 1 2 100 hg38.150200.bed.split18268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18269 0 1 2 100 hg38.150200.bed.split18269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1827 0 1 2 100 hg38.150200.bed.split1827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18270 0 1 2 100 hg38.150200.bed.split18270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18271 0 1 2 100 hg38.150200.bed.split18271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18272 0 1 2 100 hg38.150200.bed.split18272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18273 0 1 2 100 hg38.150200.bed.split18273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18274 0 1 2 100 hg38.150200.bed.split18274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18275 0 1 2 100 hg38.150200.bed.split18275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18276 0 1 2 100 hg38.150200.bed.split18276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18277 0 1 2 100 hg38.150200.bed.split18277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18278 0 1 2 100 hg38.150200.bed.split18278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18279 0 1 2 100 hg38.150200.bed.split18279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1828 0 1 2 100 hg38.150200.bed.split1828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18280 0 1 2 100 hg38.150200.bed.split18280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18281 0 1 2 100 hg38.150200.bed.split18281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18282 0 1 2 100 hg38.150200.bed.split18282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18283 0 1 2 100 hg38.150200.bed.split18283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18284 0 1 2 100 hg38.150200.bed.split18284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18285 0 1 2 100 hg38.150200.bed.split18285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18286 0 1 2 100 hg38.150200.bed.split18286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18287 0 1 2 100 hg38.150200.bed.split18287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18288 0 1 2 100 hg38.150200.bed.split18288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18289 0 1 2 100 hg38.150200.bed.split18289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1829 0 1 2 100 hg38.150200.bed.split1829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18290 0 1 2 100 hg38.150200.bed.split18290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18291 0 1 2 100 hg38.150200.bed.split18291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18292 0 1 2 100 hg38.150200.bed.split18292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18293 0 1 2 100 hg38.150200.bed.split18293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18294 0 1 2 100 hg38.150200.bed.split18294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18295 0 1 2 100 hg38.150200.bed.split18295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18296 0 1 2 100 hg38.150200.bed.split18296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18297 0 1 2 100 hg38.150200.bed.split18297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18298 0 1 2 100 hg38.150200.bed.split18298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18299 0 1 2 100 hg38.150200.bed.split18299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split183 0 1 2 100 hg38.150200.bed.split183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1830 0 1 2 100 hg38.150200.bed.split1830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18300 0 1 2 100 hg38.150200.bed.split18300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18301 0 1 2 100 hg38.150200.bed.split18301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18302 0 1 2 100 hg38.150200.bed.split18302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18303 0 1 2 100 hg38.150200.bed.split18303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18304 0 1 2 100 hg38.150200.bed.split18304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18305 0 1 2 100 hg38.150200.bed.split18305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18306 0 1 2 100 hg38.150200.bed.split18306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18307 0 1 2 100 hg38.150200.bed.split18307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18308 0 1 2 100 hg38.150200.bed.split18308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18309 0 1 2 100 hg38.150200.bed.split18309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1831 0 1 2 100 hg38.150200.bed.split1831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18310 0 1 2 100 hg38.150200.bed.split18310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18311 0 1 2 100 hg38.150200.bed.split18311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18312 0 1 2 100 hg38.150200.bed.split18312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18313 0 1 2 100 hg38.150200.bed.split18313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18314 0 1 2 100 hg38.150200.bed.split18314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18315 0 1 2 100 hg38.150200.bed.split18315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18316 0 1 2 100 hg38.150200.bed.split18316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18317 0 1 2 100 hg38.150200.bed.split18317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18318 0 1 2 100 hg38.150200.bed.split18318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18319 0 1 2 100 hg38.150200.bed.split18319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1832 0 1 2 100 hg38.150200.bed.split1832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18320 0 1 2 100 hg38.150200.bed.split18320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18321 0 1 2 100 hg38.150200.bed.split18321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18322 0 1 2 100 hg38.150200.bed.split18322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18323 0 1 2 100 hg38.150200.bed.split18323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18324 0 1 2 100 hg38.150200.bed.split18324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18325 0 1 2 100 hg38.150200.bed.split18325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18326 0 1 2 100 hg38.150200.bed.split18326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18327 0 1 2 100 hg38.150200.bed.split18327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18328 0 1 2 100 hg38.150200.bed.split18328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18329 0 1 2 100 hg38.150200.bed.split18329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1833 0 1 2 100 hg38.150200.bed.split1833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18330 0 1 2 100 hg38.150200.bed.split18330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18331 0 1 2 100 hg38.150200.bed.split18331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18332 0 1 2 100 hg38.150200.bed.split18332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18333 0 1 2 100 hg38.150200.bed.split18333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18334 0 1 2 100 hg38.150200.bed.split18334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18335 0 1 2 100 hg38.150200.bed.split18335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18336 0 1 2 100 hg38.150200.bed.split18336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18337 0 1 2 100 hg38.150200.bed.split18337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18338 0 1 2 100 hg38.150200.bed.split18338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18339 0 1 2 100 hg38.150200.bed.split18339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1834 0 1 2 100 hg38.150200.bed.split1834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18340 0 1 2 100 hg38.150200.bed.split18340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18341 0 1 2 100 hg38.150200.bed.split18341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18342 0 1 2 100 hg38.150200.bed.split18342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18343 0 1 2 100 hg38.150200.bed.split18343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18344 0 1 2 100 hg38.150200.bed.split18344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18345 0 1 2 100 hg38.150200.bed.split18345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18346 0 1 2 100 hg38.150200.bed.split18346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18347 0 1 2 100 hg38.150200.bed.split18347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18348 0 1 2 100 hg38.150200.bed.split18348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18349 0 1 2 100 hg38.150200.bed.split18349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1835 0 1 2 100 hg38.150200.bed.split1835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18350 0 1 2 100 hg38.150200.bed.split18350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18351 0 1 2 100 hg38.150200.bed.split18351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18352 0 1 2 100 hg38.150200.bed.split18352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18353 0 1 2 100 hg38.150200.bed.split18353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18354 0 1 2 100 hg38.150200.bed.split18354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18355 0 1 2 100 hg38.150200.bed.split18355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18356 0 1 2 100 hg38.150200.bed.split18356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18357 0 1 2 100 hg38.150200.bed.split18357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18358 0 1 2 100 hg38.150200.bed.split18358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18359 0 1 2 100 hg38.150200.bed.split18359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1836 0 1 2 100 hg38.150200.bed.split1836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18360 0 1 2 100 hg38.150200.bed.split18360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18361 0 1 2 100 hg38.150200.bed.split18361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18362 0 1 2 100 hg38.150200.bed.split18362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18363 0 1 2 100 hg38.150200.bed.split18363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18364 0 1 2 100 hg38.150200.bed.split18364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18365 0 1 2 100 hg38.150200.bed.split18365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18366 0 1 2 100 hg38.150200.bed.split18366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18367 0 1 2 100 hg38.150200.bed.split18367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18368 0 1 2 100 hg38.150200.bed.split18368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18369 0 1 2 100 hg38.150200.bed.split18369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1837 0 1 2 100 hg38.150200.bed.split1837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18370 0 1 2 100 hg38.150200.bed.split18370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18371 0 1 2 100 hg38.150200.bed.split18371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18372 0 1 2 100 hg38.150200.bed.split18372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18373 0 1 2 100 hg38.150200.bed.split18373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18374 0 1 2 100 hg38.150200.bed.split18374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18375 0 1 2 100 hg38.150200.bed.split18375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18376 0 1 2 100 hg38.150200.bed.split18376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18377 0 1 2 100 hg38.150200.bed.split18377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18378 0 1 2 100 hg38.150200.bed.split18378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18379 0 1 2 100 hg38.150200.bed.split18379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1838 0 1 2 100 hg38.150200.bed.split1838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18380 0 1 2 100 hg38.150200.bed.split18380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18381 0 1 2 100 hg38.150200.bed.split18381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18382 0 1 2 100 hg38.150200.bed.split18382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18383 0 1 2 100 hg38.150200.bed.split18383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18384 0 1 2 100 hg38.150200.bed.split18384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18385 0 1 2 100 hg38.150200.bed.split18385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18386 0 1 2 100 hg38.150200.bed.split18386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18387 0 1 2 100 hg38.150200.bed.split18387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18388 0 1 2 100 hg38.150200.bed.split18388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18389 0 1 2 100 hg38.150200.bed.split18389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1839 0 1 2 100 hg38.150200.bed.split1839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18390 0 1 2 100 hg38.150200.bed.split18390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18391 0 1 2 100 hg38.150200.bed.split18391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18392 0 1 2 100 hg38.150200.bed.split18392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18393 0 1 2 100 hg38.150200.bed.split18393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18394 0 1 2 100 hg38.150200.bed.split18394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18395 0 1 2 100 hg38.150200.bed.split18395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18396 0 1 2 100 hg38.150200.bed.split18396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18397 0 1 2 100 hg38.150200.bed.split18397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18398 0 1 2 100 hg38.150200.bed.split18398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18399 0 1 2 100 hg38.150200.bed.split18399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split184 0 1 2 100 hg38.150200.bed.split184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1840 0 1 2 100 hg38.150200.bed.split1840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18400 0 1 2 100 hg38.150200.bed.split18400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18401 0 1 2 100 hg38.150200.bed.split18401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18402 0 1 2 100 hg38.150200.bed.split18402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18403 0 1 2 100 hg38.150200.bed.split18403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18404 0 1 2 100 hg38.150200.bed.split18404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18405 0 1 2 100 hg38.150200.bed.split18405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18406 0 1 2 100 hg38.150200.bed.split18406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18407 0 1 2 100 hg38.150200.bed.split18407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18408 0 1 2 100 hg38.150200.bed.split18408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18409 0 1 2 100 hg38.150200.bed.split18409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1841 0 1 2 100 hg38.150200.bed.split1841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18410 0 1 2 100 hg38.150200.bed.split18410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18411 0 1 2 100 hg38.150200.bed.split18411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18412 0 1 2 100 hg38.150200.bed.split18412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18413 0 1 2 100 hg38.150200.bed.split18413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18414 0 1 2 100 hg38.150200.bed.split18414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18415 0 1 2 100 hg38.150200.bed.split18415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18416 0 1 2 100 hg38.150200.bed.split18416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18417 0 1 2 100 hg38.150200.bed.split18417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18418 0 1 2 100 hg38.150200.bed.split18418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18419 0 1 2 100 hg38.150200.bed.split18419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1842 0 1 2 100 hg38.150200.bed.split1842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18420 0 1 2 100 hg38.150200.bed.split18420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18421 0 1 2 100 hg38.150200.bed.split18421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18422 0 1 2 100 hg38.150200.bed.split18422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18423 0 1 2 100 hg38.150200.bed.split18423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18424 0 1 2 100 hg38.150200.bed.split18424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18425 0 1 2 100 hg38.150200.bed.split18425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18426 0 1 2 100 hg38.150200.bed.split18426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18427 0 1 2 100 hg38.150200.bed.split18427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18428 0 1 2 100 hg38.150200.bed.split18428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18429 0 1 2 100 hg38.150200.bed.split18429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1843 0 1 2 100 hg38.150200.bed.split1843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18430 0 1 2 100 hg38.150200.bed.split18430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18431 0 1 2 100 hg38.150200.bed.split18431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18432 0 1 2 100 hg38.150200.bed.split18432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18433 0 1 2 100 hg38.150200.bed.split18433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18434 0 1 2 100 hg38.150200.bed.split18434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18435 0 1 2 100 hg38.150200.bed.split18435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18436 0 1 2 100 hg38.150200.bed.split18436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18437 0 1 2 100 hg38.150200.bed.split18437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18438 0 1 2 100 hg38.150200.bed.split18438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18439 0 1 2 100 hg38.150200.bed.split18439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1844 0 1 2 100 hg38.150200.bed.split1844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18440 0 1 2 100 hg38.150200.bed.split18440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18441 0 1 2 100 hg38.150200.bed.split18441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18442 0 1 2 100 hg38.150200.bed.split18442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18443 0 1 2 100 hg38.150200.bed.split18443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18444 0 1 2 100 hg38.150200.bed.split18444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18445 0 1 2 100 hg38.150200.bed.split18445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18446 0 1 2 100 hg38.150200.bed.split18446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18447 0 1 2 100 hg38.150200.bed.split18447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18448 0 1 2 100 hg38.150200.bed.split18448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18449 0 1 2 100 hg38.150200.bed.split18449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1845 0 1 2 100 hg38.150200.bed.split1845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18450 0 1 2 100 hg38.150200.bed.split18450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18451 0 1 2 100 hg38.150200.bed.split18451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18452 0 1 2 100 hg38.150200.bed.split18452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18453 0 1 2 100 hg38.150200.bed.split18453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18454 0 1 2 100 hg38.150200.bed.split18454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18455 0 1 2 100 hg38.150200.bed.split18455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18456 0 1 2 100 hg38.150200.bed.split18456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18457 0 1 2 100 hg38.150200.bed.split18457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18458 0 1 2 100 hg38.150200.bed.split18458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18459 0 1 2 100 hg38.150200.bed.split18459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1846 0 1 2 100 hg38.150200.bed.split1846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18460 0 1 2 100 hg38.150200.bed.split18460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18461 0 1 2 100 hg38.150200.bed.split18461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18462 0 1 2 100 hg38.150200.bed.split18462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18463 0 1 2 100 hg38.150200.bed.split18463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18464 0 1 2 100 hg38.150200.bed.split18464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18465 0 1 2 100 hg38.150200.bed.split18465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18466 0 1 2 100 hg38.150200.bed.split18466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18467 0 1 2 100 hg38.150200.bed.split18467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18468 0 1 2 100 hg38.150200.bed.split18468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18469 0 1 2 100 hg38.150200.bed.split18469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1847 0 1 2 100 hg38.150200.bed.split1847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18470 0 1 2 100 hg38.150200.bed.split18470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18471 0 1 2 100 hg38.150200.bed.split18471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18472 0 1 2 100 hg38.150200.bed.split18472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18473 0 1 2 100 hg38.150200.bed.split18473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18474 0 1 2 100 hg38.150200.bed.split18474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18475 0 1 2 100 hg38.150200.bed.split18475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18476 0 1 2 100 hg38.150200.bed.split18476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18477 0 1 2 100 hg38.150200.bed.split18477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18478 0 1 2 100 hg38.150200.bed.split18478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18479 0 1 2 100 hg38.150200.bed.split18479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1848 0 1 2 100 hg38.150200.bed.split1848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18480 0 1 2 100 hg38.150200.bed.split18480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18481 0 1 2 100 hg38.150200.bed.split18481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18482 0 1 2 100 hg38.150200.bed.split18482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18483 0 1 2 100 hg38.150200.bed.split18483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18484 0 1 2 100 hg38.150200.bed.split18484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18485 0 1 2 100 hg38.150200.bed.split18485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18486 0 1 2 100 hg38.150200.bed.split18486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18487 0 1 2 100 hg38.150200.bed.split18487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18488 0 1 2 100 hg38.150200.bed.split18488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18489 0 1 2 100 hg38.150200.bed.split18489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1849 0 1 2 100 hg38.150200.bed.split1849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18490 0 1 2 100 hg38.150200.bed.split18490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18491 0 1 2 100 hg38.150200.bed.split18491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18492 0 1 2 100 hg38.150200.bed.split18492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18493 0 1 2 100 hg38.150200.bed.split18493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18494 0 1 2 100 hg38.150200.bed.split18494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18495 0 1 2 100 hg38.150200.bed.split18495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18496 0 1 2 100 hg38.150200.bed.split18496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18497 0 1 2 100 hg38.150200.bed.split18497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18498 0 1 2 100 hg38.150200.bed.split18498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18499 0 1 2 100 hg38.150200.bed.split18499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split185 0 1 2 100 hg38.150200.bed.split185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1850 0 1 2 100 hg38.150200.bed.split1850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18500 0 1 2 100 hg38.150200.bed.split18500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18501 0 1 2 100 hg38.150200.bed.split18501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18502 0 1 2 100 hg38.150200.bed.split18502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18503 0 1 2 100 hg38.150200.bed.split18503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18504 0 1 2 100 hg38.150200.bed.split18504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18505 0 1 2 100 hg38.150200.bed.split18505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18506 0 1 2 100 hg38.150200.bed.split18506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18507 0 1 2 100 hg38.150200.bed.split18507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18508 0 1 2 100 hg38.150200.bed.split18508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18509 0 1 2 100 hg38.150200.bed.split18509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1851 0 1 2 100 hg38.150200.bed.split1851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18510 0 1 2 100 hg38.150200.bed.split18510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18511 0 1 2 100 hg38.150200.bed.split18511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18512 0 1 2 100 hg38.150200.bed.split18512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18513 0 1 2 100 hg38.150200.bed.split18513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18514 0 1 2 100 hg38.150200.bed.split18514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18515 0 1 2 100 hg38.150200.bed.split18515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18516 0 1 2 100 hg38.150200.bed.split18516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18517 0 1 2 100 hg38.150200.bed.split18517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18518 0 1 2 100 hg38.150200.bed.split18518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18519 0 1 2 100 hg38.150200.bed.split18519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1852 0 1 2 100 hg38.150200.bed.split1852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18520 0 1 2 100 hg38.150200.bed.split18520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18521 0 1 2 100 hg38.150200.bed.split18521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18522 0 1 2 100 hg38.150200.bed.split18522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18523 0 1 2 100 hg38.150200.bed.split18523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18524 0 1 2 100 hg38.150200.bed.split18524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18525 0 1 2 100 hg38.150200.bed.split18525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18526 0 1 2 100 hg38.150200.bed.split18526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18527 0 1 2 100 hg38.150200.bed.split18527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18528 0 1 2 100 hg38.150200.bed.split18528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18529 0 1 2 100 hg38.150200.bed.split18529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1853 0 1 2 100 hg38.150200.bed.split1853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18530 0 1 2 100 hg38.150200.bed.split18530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18531 0 1 2 100 hg38.150200.bed.split18531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18532 0 1 2 100 hg38.150200.bed.split18532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18533 0 1 2 100 hg38.150200.bed.split18533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18534 0 1 2 100 hg38.150200.bed.split18534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18535 0 1 2 100 hg38.150200.bed.split18535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18536 0 1 2 100 hg38.150200.bed.split18536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18537 0 1 2 100 hg38.150200.bed.split18537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18538 0 1 2 100 hg38.150200.bed.split18538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18539 0 1 2 100 hg38.150200.bed.split18539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1854 0 1 2 100 hg38.150200.bed.split1854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18540 0 1 2 100 hg38.150200.bed.split18540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18541 0 1 2 100 hg38.150200.bed.split18541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18542 0 1 2 100 hg38.150200.bed.split18542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18543 0 1 2 100 hg38.150200.bed.split18543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18544 0 1 2 100 hg38.150200.bed.split18544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18545 0 1 2 100 hg38.150200.bed.split18545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18546 0 1 2 100 hg38.150200.bed.split18546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18547 0 1 2 100 hg38.150200.bed.split18547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18548 0 1 2 100 hg38.150200.bed.split18548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18549 0 1 2 100 hg38.150200.bed.split18549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1855 0 1 2 100 hg38.150200.bed.split1855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18550 0 1 2 100 hg38.150200.bed.split18550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18551 0 1 2 100 hg38.150200.bed.split18551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18552 0 1 2 100 hg38.150200.bed.split18552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18553 0 1 2 100 hg38.150200.bed.split18553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18554 0 1 2 100 hg38.150200.bed.split18554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18555 0 1 2 100 hg38.150200.bed.split18555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18556 0 1 2 100 hg38.150200.bed.split18556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18557 0 1 2 100 hg38.150200.bed.split18557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18558 0 1 2 100 hg38.150200.bed.split18558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18559 0 1 2 100 hg38.150200.bed.split18559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1856 0 1 2 100 hg38.150200.bed.split1856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18560 0 1 2 100 hg38.150200.bed.split18560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18561 0 1 2 100 hg38.150200.bed.split18561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18562 0 1 2 100 hg38.150200.bed.split18562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18563 0 1 2 100 hg38.150200.bed.split18563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18564 0 1 2 100 hg38.150200.bed.split18564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18565 0 1 2 100 hg38.150200.bed.split18565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18566 0 1 2 100 hg38.150200.bed.split18566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18567 0 1 2 100 hg38.150200.bed.split18567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18568 0 1 2 100 hg38.150200.bed.split18568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18569 0 1 2 100 hg38.150200.bed.split18569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1857 0 1 2 100 hg38.150200.bed.split1857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18570 0 1 2 100 hg38.150200.bed.split18570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18571 0 1 2 100 hg38.150200.bed.split18571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18572 0 1 2 100 hg38.150200.bed.split18572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18573 0 1 2 100 hg38.150200.bed.split18573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18574 0 1 2 100 hg38.150200.bed.split18574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18575 0 1 2 100 hg38.150200.bed.split18575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18576 0 1 2 100 hg38.150200.bed.split18576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18577 0 1 2 100 hg38.150200.bed.split18577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18578 0 1 2 100 hg38.150200.bed.split18578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18579 0 1 2 100 hg38.150200.bed.split18579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1858 0 1 2 100 hg38.150200.bed.split1858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18580 0 1 2 100 hg38.150200.bed.split18580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18581 0 1 2 100 hg38.150200.bed.split18581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18582 0 1 2 100 hg38.150200.bed.split18582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18583 0 1 2 100 hg38.150200.bed.split18583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18584 0 1 2 100 hg38.150200.bed.split18584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18585 0 1 2 100 hg38.150200.bed.split18585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18586 0 1 2 100 hg38.150200.bed.split18586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18587 0 1 2 100 hg38.150200.bed.split18587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18588 0 1 2 100 hg38.150200.bed.split18588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18589 0 1 2 100 hg38.150200.bed.split18589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1859 0 1 2 100 hg38.150200.bed.split1859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18590 0 1 2 100 hg38.150200.bed.split18590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18591 0 1 2 100 hg38.150200.bed.split18591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18592 0 1 2 100 hg38.150200.bed.split18592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18593 0 1 2 100 hg38.150200.bed.split18593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18594 0 1 2 100 hg38.150200.bed.split18594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18595 0 1 2 100 hg38.150200.bed.split18595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18596 0 1 2 100 hg38.150200.bed.split18596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18597 0 1 2 100 hg38.150200.bed.split18597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18598 0 1 2 100 hg38.150200.bed.split18598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18599 0 1 2 100 hg38.150200.bed.split18599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split186 0 1 2 100 hg38.150200.bed.split186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1860 0 1 2 100 hg38.150200.bed.split1860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18600 0 1 2 100 hg38.150200.bed.split18600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18601 0 1 2 100 hg38.150200.bed.split18601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18602 0 1 2 100 hg38.150200.bed.split18602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18603 0 1 2 100 hg38.150200.bed.split18603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18604 0 1 2 100 hg38.150200.bed.split18604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18605 0 1 2 100 hg38.150200.bed.split18605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18606 0 1 2 100 hg38.150200.bed.split18606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18607 0 1 2 100 hg38.150200.bed.split18607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18608 0 1 2 100 hg38.150200.bed.split18608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18609 0 1 2 100 hg38.150200.bed.split18609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1861 0 1 2 100 hg38.150200.bed.split1861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18610 0 1 2 100 hg38.150200.bed.split18610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18611 0 1 2 100 hg38.150200.bed.split18611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18612 0 1 2 100 hg38.150200.bed.split18612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18613 0 1 2 100 hg38.150200.bed.split18613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18614 0 1 2 100 hg38.150200.bed.split18614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18615 0 1 2 100 hg38.150200.bed.split18615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18616 0 1 2 100 hg38.150200.bed.split18616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18617 0 1 2 100 hg38.150200.bed.split18617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18618 0 1 2 100 hg38.150200.bed.split18618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18619 0 1 2 100 hg38.150200.bed.split18619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1862 0 1 2 100 hg38.150200.bed.split1862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18620 0 1 2 100 hg38.150200.bed.split18620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18621 0 1 2 100 hg38.150200.bed.split18621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18622 0 1 2 100 hg38.150200.bed.split18622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18623 0 1 2 100 hg38.150200.bed.split18623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18624 0 1 2 100 hg38.150200.bed.split18624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18625 0 1 2 100 hg38.150200.bed.split18625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18626 0 1 2 100 hg38.150200.bed.split18626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18627 0 1 2 100 hg38.150200.bed.split18627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18628 0 1 2 100 hg38.150200.bed.split18628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18629 0 1 2 100 hg38.150200.bed.split18629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1863 0 1 2 100 hg38.150200.bed.split1863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18630 0 1 2 100 hg38.150200.bed.split18630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18631 0 1 2 100 hg38.150200.bed.split18631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18632 0 1 2 100 hg38.150200.bed.split18632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18633 0 1 2 100 hg38.150200.bed.split18633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18634 0 1 2 100 hg38.150200.bed.split18634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18635 0 1 2 100 hg38.150200.bed.split18635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18636 0 1 2 100 hg38.150200.bed.split18636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18637 0 1 2 100 hg38.150200.bed.split18637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18638 0 1 2 100 hg38.150200.bed.split18638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18639 0 1 2 100 hg38.150200.bed.split18639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1864 0 1 2 100 hg38.150200.bed.split1864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18640 0 1 2 100 hg38.150200.bed.split18640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18641 0 1 2 100 hg38.150200.bed.split18641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18642 0 1 2 100 hg38.150200.bed.split18642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18643 0 1 2 100 hg38.150200.bed.split18643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18644 0 1 2 100 hg38.150200.bed.split18644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18645 0 1 2 100 hg38.150200.bed.split18645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18646 0 1 2 100 hg38.150200.bed.split18646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18647 0 1 2 100 hg38.150200.bed.split18647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18648 0 1 2 100 hg38.150200.bed.split18648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18649 0 1 2 100 hg38.150200.bed.split18649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1865 0 1 2 100 hg38.150200.bed.split1865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18650 0 1 2 100 hg38.150200.bed.split18650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18651 0 1 2 100 hg38.150200.bed.split18651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18652 0 1 2 100 hg38.150200.bed.split18652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18653 0 1 2 100 hg38.150200.bed.split18653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18654 0 1 2 100 hg38.150200.bed.split18654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18655 0 1 2 100 hg38.150200.bed.split18655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18656 0 1 2 100 hg38.150200.bed.split18656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18657 0 1 2 100 hg38.150200.bed.split18657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18658 0 1 2 100 hg38.150200.bed.split18658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18659 0 1 2 100 hg38.150200.bed.split18659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1866 0 1 2 100 hg38.150200.bed.split1866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18660 0 1 2 100 hg38.150200.bed.split18660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18661 0 1 2 100 hg38.150200.bed.split18661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18662 0 1 2 100 hg38.150200.bed.split18662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18663 0 1 2 100 hg38.150200.bed.split18663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18664 0 1 2 100 hg38.150200.bed.split18664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18665 0 1 2 100 hg38.150200.bed.split18665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18666 0 1 2 100 hg38.150200.bed.split18666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18667 0 1 2 100 hg38.150200.bed.split18667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18668 0 1 2 100 hg38.150200.bed.split18668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18669 0 1 2 100 hg38.150200.bed.split18669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1867 0 1 2 100 hg38.150200.bed.split1867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18670 0 1 2 100 hg38.150200.bed.split18670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18671 0 1 2 100 hg38.150200.bed.split18671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18672 0 1 2 100 hg38.150200.bed.split18672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18673 0 1 2 100 hg38.150200.bed.split18673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18674 0 1 2 100 hg38.150200.bed.split18674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18675 0 1 2 100 hg38.150200.bed.split18675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18676 0 1 2 100 hg38.150200.bed.split18676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18677 0 1 2 100 hg38.150200.bed.split18677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18678 0 1 2 100 hg38.150200.bed.split18678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18679 0 1 2 100 hg38.150200.bed.split18679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1868 0 1 2 100 hg38.150200.bed.split1868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18680 0 1 2 100 hg38.150200.bed.split18680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18681 0 1 2 100 hg38.150200.bed.split18681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18682 0 1 2 100 hg38.150200.bed.split18682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18683 0 1 2 100 hg38.150200.bed.split18683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18684 0 1 2 100 hg38.150200.bed.split18684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18685 0 1 2 100 hg38.150200.bed.split18685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18686 0 1 2 100 hg38.150200.bed.split18686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18687 0 1 2 100 hg38.150200.bed.split18687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18688 0 1 2 100 hg38.150200.bed.split18688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18689 0 1 2 100 hg38.150200.bed.split18689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1869 0 1 2 100 hg38.150200.bed.split1869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18690 0 1 2 100 hg38.150200.bed.split18690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18691 0 1 2 100 hg38.150200.bed.split18691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18692 0 1 2 100 hg38.150200.bed.split18692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18693 0 1 2 100 hg38.150200.bed.split18693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18694 0 1 2 100 hg38.150200.bed.split18694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18695 0 1 2 100 hg38.150200.bed.split18695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18696 0 1 2 100 hg38.150200.bed.split18696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18697 0 1 2 100 hg38.150200.bed.split18697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18698 0 1 2 100 hg38.150200.bed.split18698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18699 0 1 2 100 hg38.150200.bed.split18699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split187 0 1 2 100 hg38.150200.bed.split187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1870 0 1 2 100 hg38.150200.bed.split1870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18700 0 1 2 100 hg38.150200.bed.split18700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18701 0 1 2 100 hg38.150200.bed.split18701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18702 0 1 2 100 hg38.150200.bed.split18702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18703 0 1 2 100 hg38.150200.bed.split18703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18704 0 1 2 100 hg38.150200.bed.split18704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18705 0 1 2 100 hg38.150200.bed.split18705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18706 0 1 2 100 hg38.150200.bed.split18706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18707 0 1 2 100 hg38.150200.bed.split18707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18708 0 1 2 100 hg38.150200.bed.split18708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18709 0 1 2 100 hg38.150200.bed.split18709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1871 0 1 2 100 hg38.150200.bed.split1871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18710 0 1 2 100 hg38.150200.bed.split18710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18711 0 1 2 100 hg38.150200.bed.split18711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18712 0 1 2 100 hg38.150200.bed.split18712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18713 0 1 2 100 hg38.150200.bed.split18713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18714 0 1 2 100 hg38.150200.bed.split18714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18715 0 1 2 100 hg38.150200.bed.split18715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18716 0 1 2 100 hg38.150200.bed.split18716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18717 0 1 2 100 hg38.150200.bed.split18717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18718 0 1 2 100 hg38.150200.bed.split18718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18719 0 1 2 100 hg38.150200.bed.split18719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1872 0 1 2 100 hg38.150200.bed.split1872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18720 0 1 2 100 hg38.150200.bed.split18720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18721 0 1 2 100 hg38.150200.bed.split18721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18722 0 1 2 100 hg38.150200.bed.split18722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18723 0 1 2 100 hg38.150200.bed.split18723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18724 0 1 2 100 hg38.150200.bed.split18724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18725 0 1 2 100 hg38.150200.bed.split18725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18726 0 1 2 100 hg38.150200.bed.split18726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18727 0 1 2 100 hg38.150200.bed.split18727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18728 0 1 2 100 hg38.150200.bed.split18728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18729 0 1 2 100 hg38.150200.bed.split18729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1873 0 1 2 100 hg38.150200.bed.split1873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18730 0 1 2 100 hg38.150200.bed.split18730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18731 0 1 2 100 hg38.150200.bed.split18731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18732 0 1 2 100 hg38.150200.bed.split18732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18733 0 1 2 100 hg38.150200.bed.split18733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18734 0 1 2 100 hg38.150200.bed.split18734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18735 0 1 2 100 hg38.150200.bed.split18735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18736 0 1 2 100 hg38.150200.bed.split18736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18737 0 1 2 100 hg38.150200.bed.split18737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18738 0 1 2 100 hg38.150200.bed.split18738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18739 0 1 2 100 hg38.150200.bed.split18739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1874 0 1 2 100 hg38.150200.bed.split1874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18740 0 1 2 100 hg38.150200.bed.split18740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18741 0 1 2 100 hg38.150200.bed.split18741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18742 0 1 2 100 hg38.150200.bed.split18742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18743 0 1 2 100 hg38.150200.bed.split18743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18744 0 1 2 100 hg38.150200.bed.split18744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18745 0 1 2 100 hg38.150200.bed.split18745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18746 0 1 2 100 hg38.150200.bed.split18746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18747 0 1 2 100 hg38.150200.bed.split18747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18748 0 1 2 100 hg38.150200.bed.split18748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18749 0 1 2 100 hg38.150200.bed.split18749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1875 0 1 2 100 hg38.150200.bed.split1875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18750 0 1 2 100 hg38.150200.bed.split18750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18751 0 1 2 100 hg38.150200.bed.split18751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18752 0 1 2 100 hg38.150200.bed.split18752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18753 0 1 2 100 hg38.150200.bed.split18753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18754 0 1 2 100 hg38.150200.bed.split18754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18755 0 1 2 100 hg38.150200.bed.split18755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18756 0 1 2 100 hg38.150200.bed.split18756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18757 0 1 2 100 hg38.150200.bed.split18757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18758 0 1 2 100 hg38.150200.bed.split18758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18759 0 1 2 100 hg38.150200.bed.split18759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1876 0 1 2 100 hg38.150200.bed.split1876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18760 0 1 2 100 hg38.150200.bed.split18760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18761 0 1 2 100 hg38.150200.bed.split18761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18762 0 1 2 100 hg38.150200.bed.split18762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18763 0 1 2 100 hg38.150200.bed.split18763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18764 0 1 2 100 hg38.150200.bed.split18764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18765 0 1 2 100 hg38.150200.bed.split18765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18766 0 1 2 100 hg38.150200.bed.split18766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18767 0 1 2 100 hg38.150200.bed.split18767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18768 0 1 2 100 hg38.150200.bed.split18768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18769 0 1 2 100 hg38.150200.bed.split18769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1877 0 1 2 100 hg38.150200.bed.split1877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18770 0 1 2 100 hg38.150200.bed.split18770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18771 0 1 2 100 hg38.150200.bed.split18771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18772 0 1 2 100 hg38.150200.bed.split18772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18773 0 1 2 100 hg38.150200.bed.split18773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18774 0 1 2 100 hg38.150200.bed.split18774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18775 0 1 2 100 hg38.150200.bed.split18775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18776 0 1 2 100 hg38.150200.bed.split18776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18777 0 1 2 100 hg38.150200.bed.split18777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18778 0 1 2 100 hg38.150200.bed.split18778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18779 0 1 2 100 hg38.150200.bed.split18779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1878 0 1 2 100 hg38.150200.bed.split1878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18780 0 1 2 100 hg38.150200.bed.split18780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18781 0 1 2 100 hg38.150200.bed.split18781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18782 0 1 2 100 hg38.150200.bed.split18782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18783 0 1 2 100 hg38.150200.bed.split18783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18784 0 1 2 100 hg38.150200.bed.split18784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18785 0 1 2 100 hg38.150200.bed.split18785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18786 0 1 2 100 hg38.150200.bed.split18786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18787 0 1 2 100 hg38.150200.bed.split18787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18788 0 1 2 100 hg38.150200.bed.split18788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18789 0 1 2 100 hg38.150200.bed.split18789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1879 0 1 2 100 hg38.150200.bed.split1879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18790 0 1 2 100 hg38.150200.bed.split18790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18791 0 1 2 100 hg38.150200.bed.split18791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18792 0 1 2 100 hg38.150200.bed.split18792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18793 0 1 2 100 hg38.150200.bed.split18793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18794 0 1 2 100 hg38.150200.bed.split18794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18795 0 1 2 100 hg38.150200.bed.split18795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18796 0 1 2 100 hg38.150200.bed.split18796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18797 0 1 2 100 hg38.150200.bed.split18797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18798 0 1 2 100 hg38.150200.bed.split18798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18799 0 1 2 100 hg38.150200.bed.split18799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split188 0 1 2 100 hg38.150200.bed.split188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1880 0 1 2 100 hg38.150200.bed.split1880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18800 0 1 2 100 hg38.150200.bed.split18800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18801 0 1 2 100 hg38.150200.bed.split18801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18802 0 1 2 100 hg38.150200.bed.split18802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18803 0 1 2 100 hg38.150200.bed.split18803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18804 0 1 2 100 hg38.150200.bed.split18804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18805 0 1 2 100 hg38.150200.bed.split18805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18806 0 1 2 100 hg38.150200.bed.split18806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18807 0 1 2 100 hg38.150200.bed.split18807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18808 0 1 2 100 hg38.150200.bed.split18808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18809 0 1 2 100 hg38.150200.bed.split18809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1881 0 1 2 100 hg38.150200.bed.split1881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18810 0 1 2 100 hg38.150200.bed.split18810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18811 0 1 2 100 hg38.150200.bed.split18811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18812 0 1 2 100 hg38.150200.bed.split18812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18813 0 1 2 100 hg38.150200.bed.split18813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18814 0 1 2 100 hg38.150200.bed.split18814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18815 0 1 2 100 hg38.150200.bed.split18815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18816 0 1 2 100 hg38.150200.bed.split18816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18817 0 1 2 100 hg38.150200.bed.split18817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18818 0 1 2 100 hg38.150200.bed.split18818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18819 0 1 2 100 hg38.150200.bed.split18819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1882 0 1 2 100 hg38.150200.bed.split1882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18820 0 1 2 100 hg38.150200.bed.split18820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18821 0 1 2 100 hg38.150200.bed.split18821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18822 0 1 2 100 hg38.150200.bed.split18822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18823 0 1 2 100 hg38.150200.bed.split18823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18824 0 1 2 100 hg38.150200.bed.split18824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18825 0 1 2 100 hg38.150200.bed.split18825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18826 0 1 2 100 hg38.150200.bed.split18826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18827 0 1 2 100 hg38.150200.bed.split18827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18828 0 1 2 100 hg38.150200.bed.split18828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18829 0 1 2 100 hg38.150200.bed.split18829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1883 0 1 2 100 hg38.150200.bed.split1883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18830 0 1 2 100 hg38.150200.bed.split18830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18831 0 1 2 100 hg38.150200.bed.split18831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18832 0 1 2 100 hg38.150200.bed.split18832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18833 0 1 2 100 hg38.150200.bed.split18833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18834 0 1 2 100 hg38.150200.bed.split18834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18835 0 1 2 100 hg38.150200.bed.split18835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18836 0 1 2 100 hg38.150200.bed.split18836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18837 0 1 2 100 hg38.150200.bed.split18837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18838 0 1 2 100 hg38.150200.bed.split18838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18839 0 1 2 100 hg38.150200.bed.split18839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1884 0 1 2 100 hg38.150200.bed.split1884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18840 0 1 2 100 hg38.150200.bed.split18840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18841 0 1 2 100 hg38.150200.bed.split18841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18842 0 1 2 100 hg38.150200.bed.split18842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18843 0 1 2 100 hg38.150200.bed.split18843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18844 0 1 2 100 hg38.150200.bed.split18844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18845 0 1 2 100 hg38.150200.bed.split18845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18846 0 1 2 100 hg38.150200.bed.split18846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18847 0 1 2 100 hg38.150200.bed.split18847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18848 0 1 2 100 hg38.150200.bed.split18848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18849 0 1 2 100 hg38.150200.bed.split18849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1885 0 1 2 100 hg38.150200.bed.split1885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18850 0 1 2 100 hg38.150200.bed.split18850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18851 0 1 2 100 hg38.150200.bed.split18851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18852 0 1 2 100 hg38.150200.bed.split18852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18853 0 1 2 100 hg38.150200.bed.split18853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18854 0 1 2 100 hg38.150200.bed.split18854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18855 0 1 2 100 hg38.150200.bed.split18855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18856 0 1 2 100 hg38.150200.bed.split18856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18857 0 1 2 100 hg38.150200.bed.split18857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18858 0 1 2 100 hg38.150200.bed.split18858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18859 0 1 2 100 hg38.150200.bed.split18859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1886 0 1 2 100 hg38.150200.bed.split1886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18860 0 1 2 100 hg38.150200.bed.split18860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18861 0 1 2 100 hg38.150200.bed.split18861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18862 0 1 2 100 hg38.150200.bed.split18862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18863 0 1 2 100 hg38.150200.bed.split18863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18864 0 1 2 100 hg38.150200.bed.split18864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18865 0 1 2 100 hg38.150200.bed.split18865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18866 0 1 2 100 hg38.150200.bed.split18866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18867 0 1 2 100 hg38.150200.bed.split18867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18868 0 1 2 100 hg38.150200.bed.split18868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18869 0 1 2 100 hg38.150200.bed.split18869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1887 0 1 2 100 hg38.150200.bed.split1887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18870 0 1 2 100 hg38.150200.bed.split18870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18871 0 1 2 100 hg38.150200.bed.split18871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18872 0 1 2 100 hg38.150200.bed.split18872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18873 0 1 2 100 hg38.150200.bed.split18873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18874 0 1 2 100 hg38.150200.bed.split18874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18875 0 1 2 100 hg38.150200.bed.split18875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18876 0 1 2 100 hg38.150200.bed.split18876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18877 0 1 2 100 hg38.150200.bed.split18877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18878 0 1 2 100 hg38.150200.bed.split18878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18879 0 1 2 100 hg38.150200.bed.split18879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1888 0 1 2 100 hg38.150200.bed.split1888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18880 0 1 2 100 hg38.150200.bed.split18880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18881 0 1 2 100 hg38.150200.bed.split18881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18882 0 1 2 100 hg38.150200.bed.split18882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18883 0 1 2 100 hg38.150200.bed.split18883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18884 0 1 2 100 hg38.150200.bed.split18884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18885 0 1 2 100 hg38.150200.bed.split18885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18886 0 1 2 100 hg38.150200.bed.split18886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18887 0 1 2 100 hg38.150200.bed.split18887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18888 0 1 2 100 hg38.150200.bed.split18888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18889 0 1 2 100 hg38.150200.bed.split18889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1889 0 1 2 100 hg38.150200.bed.split1889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18890 0 1 2 100 hg38.150200.bed.split18890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18891 0 1 2 100 hg38.150200.bed.split18891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18892 0 1 2 100 hg38.150200.bed.split18892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18893 0 1 2 100 hg38.150200.bed.split18893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18894 0 1 2 100 hg38.150200.bed.split18894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18895 0 1 2 100 hg38.150200.bed.split18895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18896 0 1 2 100 hg38.150200.bed.split18896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18897 0 1 2 100 hg38.150200.bed.split18897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18898 0 1 2 100 hg38.150200.bed.split18898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18899 0 1 2 100 hg38.150200.bed.split18899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split189 0 1 2 100 hg38.150200.bed.split189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1890 0 1 2 100 hg38.150200.bed.split1890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18900 0 1 2 100 hg38.150200.bed.split18900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18901 0 1 2 100 hg38.150200.bed.split18901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18902 0 1 2 100 hg38.150200.bed.split18902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18903 0 1 2 100 hg38.150200.bed.split18903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18904 0 1 2 100 hg38.150200.bed.split18904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18905 0 1 2 100 hg38.150200.bed.split18905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18906 0 1 2 100 hg38.150200.bed.split18906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18907 0 1 2 100 hg38.150200.bed.split18907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18908 0 1 2 100 hg38.150200.bed.split18908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18909 0 1 2 100 hg38.150200.bed.split18909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1891 0 1 2 100 hg38.150200.bed.split1891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18910 0 1 2 100 hg38.150200.bed.split18910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18911 0 1 2 100 hg38.150200.bed.split18911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18912 0 1 2 100 hg38.150200.bed.split18912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18913 0 1 2 100 hg38.150200.bed.split18913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18914 0 1 2 100 hg38.150200.bed.split18914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18915 0 1 2 100 hg38.150200.bed.split18915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18916 0 1 2 100 hg38.150200.bed.split18916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18917 0 1 2 100 hg38.150200.bed.split18917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18918 0 1 2 100 hg38.150200.bed.split18918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18919 0 1 2 100 hg38.150200.bed.split18919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1892 0 1 2 100 hg38.150200.bed.split1892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18920 0 1 2 100 hg38.150200.bed.split18920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18921 0 1 2 100 hg38.150200.bed.split18921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18922 0 1 2 100 hg38.150200.bed.split18922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18923 0 1 2 100 hg38.150200.bed.split18923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18924 0 1 2 100 hg38.150200.bed.split18924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18925 0 1 2 100 hg38.150200.bed.split18925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18926 0 1 2 100 hg38.150200.bed.split18926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18927 0 1 2 100 hg38.150200.bed.split18927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18928 0 1 2 100 hg38.150200.bed.split18928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18929 0 1 2 100 hg38.150200.bed.split18929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1893 0 1 2 100 hg38.150200.bed.split1893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18930 0 1 2 100 hg38.150200.bed.split18930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18931 0 1 2 100 hg38.150200.bed.split18931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18932 0 1 2 100 hg38.150200.bed.split18932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18933 0 1 2 100 hg38.150200.bed.split18933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18934 0 1 2 100 hg38.150200.bed.split18934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18935 0 1 2 100 hg38.150200.bed.split18935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18936 0 1 2 100 hg38.150200.bed.split18936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18937 0 1 2 100 hg38.150200.bed.split18937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18938 0 1 2 100 hg38.150200.bed.split18938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18939 0 1 2 100 hg38.150200.bed.split18939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1894 0 1 2 100 hg38.150200.bed.split1894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18940 0 1 2 100 hg38.150200.bed.split18940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18941 0 1 2 100 hg38.150200.bed.split18941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18942 0 1 2 100 hg38.150200.bed.split18942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18943 0 1 2 100 hg38.150200.bed.split18943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18944 0 1 2 100 hg38.150200.bed.split18944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18945 0 1 2 100 hg38.150200.bed.split18945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18946 0 1 2 100 hg38.150200.bed.split18946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18947 0 1 2 100 hg38.150200.bed.split18947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18948 0 1 2 100 hg38.150200.bed.split18948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18949 0 1 2 100 hg38.150200.bed.split18949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1895 0 1 2 100 hg38.150200.bed.split1895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18950 0 1 2 100 hg38.150200.bed.split18950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18951 0 1 2 100 hg38.150200.bed.split18951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18952 0 1 2 100 hg38.150200.bed.split18952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18953 0 1 2 100 hg38.150200.bed.split18953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18954 0 1 2 100 hg38.150200.bed.split18954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18955 0 1 2 100 hg38.150200.bed.split18955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18956 0 1 2 100 hg38.150200.bed.split18956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18957 0 1 2 100 hg38.150200.bed.split18957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18958 0 1 2 100 hg38.150200.bed.split18958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18959 0 1 2 100 hg38.150200.bed.split18959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1896 0 1 2 100 hg38.150200.bed.split1896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18960 0 1 2 100 hg38.150200.bed.split18960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18961 0 1 2 100 hg38.150200.bed.split18961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18962 0 1 2 100 hg38.150200.bed.split18962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18963 0 1 2 100 hg38.150200.bed.split18963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18964 0 1 2 100 hg38.150200.bed.split18964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18965 0 1 2 100 hg38.150200.bed.split18965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18966 0 1 2 100 hg38.150200.bed.split18966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18967 0 1 2 100 hg38.150200.bed.split18967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18968 0 1 2 100 hg38.150200.bed.split18968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18969 0 1 2 100 hg38.150200.bed.split18969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1897 0 1 2 100 hg38.150200.bed.split1897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18970 0 1 2 100 hg38.150200.bed.split18970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18971 0 1 2 100 hg38.150200.bed.split18971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18972 0 1 2 100 hg38.150200.bed.split18972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18973 0 1 2 100 hg38.150200.bed.split18973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18974 0 1 2 100 hg38.150200.bed.split18974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18975 0 1 2 100 hg38.150200.bed.split18975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18976 0 1 2 100 hg38.150200.bed.split18976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18977 0 1 2 100 hg38.150200.bed.split18977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18978 0 1 2 100 hg38.150200.bed.split18978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18979 0 1 2 100 hg38.150200.bed.split18979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1898 0 1 2 100 hg38.150200.bed.split1898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18980 0 1 2 100 hg38.150200.bed.split18980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18981 0 1 2 100 hg38.150200.bed.split18981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18982 0 1 2 100 hg38.150200.bed.split18982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18983 0 1 2 100 hg38.150200.bed.split18983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18984 0 1 2 100 hg38.150200.bed.split18984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18985 0 1 2 100 hg38.150200.bed.split18985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18986 0 1 2 100 hg38.150200.bed.split18986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18987 0 1 2 100 hg38.150200.bed.split18987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18988 0 1 2 100 hg38.150200.bed.split18988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18989 0 1 2 100 hg38.150200.bed.split18989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1899 0 1 2 100 hg38.150200.bed.split1899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18990 0 1 2 100 hg38.150200.bed.split18990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18991 0 1 2 100 hg38.150200.bed.split18991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18992 0 1 2 100 hg38.150200.bed.split18992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18993 0 1 2 100 hg38.150200.bed.split18993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18994 0 1 2 100 hg38.150200.bed.split18994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18995 0 1 2 100 hg38.150200.bed.split18995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18996 0 1 2 100 hg38.150200.bed.split18996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18997 0 1 2 100 hg38.150200.bed.split18997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18998 0 1 2 100 hg38.150200.bed.split18998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split18999 0 1 2 100 hg38.150200.bed.split18999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19 0 1 2 100 hg38.150200.bed.split19.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split190 0 1 2 100 hg38.150200.bed.split190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1900 0 1 2 100 hg38.150200.bed.split1900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19000 0 1 2 100 hg38.150200.bed.split19000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19001 0 1 2 100 hg38.150200.bed.split19001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19002 0 1 2 100 hg38.150200.bed.split19002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19003 0 1 2 100 hg38.150200.bed.split19003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19004 0 1 2 100 hg38.150200.bed.split19004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19005 0 1 2 100 hg38.150200.bed.split19005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19006 0 1 2 100 hg38.150200.bed.split19006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19007 0 1 2 100 hg38.150200.bed.split19007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19008 0 1 2 100 hg38.150200.bed.split19008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19009 0 1 2 100 hg38.150200.bed.split19009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1901 0 1 2 100 hg38.150200.bed.split1901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19010 0 1 2 100 hg38.150200.bed.split19010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19011 0 1 2 100 hg38.150200.bed.split19011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19012 0 1 2 100 hg38.150200.bed.split19012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19013 0 1 2 100 hg38.150200.bed.split19013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19014 0 1 2 100 hg38.150200.bed.split19014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19015 0 1 2 100 hg38.150200.bed.split19015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19016 0 1 2 100 hg38.150200.bed.split19016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19017 0 1 2 100 hg38.150200.bed.split19017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19018 0 1 2 100 hg38.150200.bed.split19018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19019 0 1 2 100 hg38.150200.bed.split19019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1902 0 1 2 100 hg38.150200.bed.split1902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19020 0 1 2 100 hg38.150200.bed.split19020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19021 0 1 2 100 hg38.150200.bed.split19021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19022 0 1 2 100 hg38.150200.bed.split19022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19023 0 1 2 100 hg38.150200.bed.split19023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19024 0 1 2 100 hg38.150200.bed.split19024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19025 0 1 2 100 hg38.150200.bed.split19025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19026 0 1 2 100 hg38.150200.bed.split19026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19027 0 1 2 100 hg38.150200.bed.split19027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19028 0 1 2 100 hg38.150200.bed.split19028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19029 0 1 2 100 hg38.150200.bed.split19029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1903 0 1 2 100 hg38.150200.bed.split1903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19030 0 1 2 100 hg38.150200.bed.split19030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19031 0 1 2 100 hg38.150200.bed.split19031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19032 0 1 2 100 hg38.150200.bed.split19032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19033 0 1 2 100 hg38.150200.bed.split19033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19034 0 1 2 100 hg38.150200.bed.split19034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19035 0 1 2 100 hg38.150200.bed.split19035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19036 0 1 2 100 hg38.150200.bed.split19036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19037 0 1 2 100 hg38.150200.bed.split19037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19038 0 1 2 100 hg38.150200.bed.split19038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19039 0 1 2 100 hg38.150200.bed.split19039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1904 0 1 2 100 hg38.150200.bed.split1904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19040 0 1 2 100 hg38.150200.bed.split19040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19041 0 1 2 100 hg38.150200.bed.split19041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19042 0 1 2 100 hg38.150200.bed.split19042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19043 0 1 2 100 hg38.150200.bed.split19043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19044 0 1 2 100 hg38.150200.bed.split19044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19045 0 1 2 100 hg38.150200.bed.split19045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19046 0 1 2 100 hg38.150200.bed.split19046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19047 0 1 2 100 hg38.150200.bed.split19047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19048 0 1 2 100 hg38.150200.bed.split19048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19049 0 1 2 100 hg38.150200.bed.split19049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1905 0 1 2 100 hg38.150200.bed.split1905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19050 0 1 2 100 hg38.150200.bed.split19050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19051 0 1 2 100 hg38.150200.bed.split19051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19052 0 1 2 100 hg38.150200.bed.split19052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19053 0 1 2 100 hg38.150200.bed.split19053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19054 0 1 2 100 hg38.150200.bed.split19054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19055 0 1 2 100 hg38.150200.bed.split19055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19056 0 1 2 100 hg38.150200.bed.split19056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19057 0 1 2 100 hg38.150200.bed.split19057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19058 0 1 2 100 hg38.150200.bed.split19058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19059 0 1 2 100 hg38.150200.bed.split19059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1906 0 1 2 100 hg38.150200.bed.split1906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19060 0 1 2 100 hg38.150200.bed.split19060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19061 0 1 2 100 hg38.150200.bed.split19061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19062 0 1 2 100 hg38.150200.bed.split19062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19063 0 1 2 100 hg38.150200.bed.split19063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19064 0 1 2 100 hg38.150200.bed.split19064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19065 0 1 2 100 hg38.150200.bed.split19065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19066 0 1 2 100 hg38.150200.bed.split19066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19067 0 1 2 100 hg38.150200.bed.split19067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19068 0 1 2 100 hg38.150200.bed.split19068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19069 0 1 2 100 hg38.150200.bed.split19069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1907 0 1 2 100 hg38.150200.bed.split1907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19070 0 1 2 100 hg38.150200.bed.split19070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19071 0 1 2 100 hg38.150200.bed.split19071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19072 0 1 2 100 hg38.150200.bed.split19072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19073 0 1 2 100 hg38.150200.bed.split19073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19074 0 1 2 100 hg38.150200.bed.split19074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19075 0 1 2 100 hg38.150200.bed.split19075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19076 0 1 2 100 hg38.150200.bed.split19076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19077 0 1 2 100 hg38.150200.bed.split19077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19078 0 1 2 100 hg38.150200.bed.split19078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19079 0 1 2 100 hg38.150200.bed.split19079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1908 0 1 2 100 hg38.150200.bed.split1908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19080 0 1 2 100 hg38.150200.bed.split19080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19081 0 1 2 100 hg38.150200.bed.split19081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19082 0 1 2 100 hg38.150200.bed.split19082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19083 0 1 2 100 hg38.150200.bed.split19083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19084 0 1 2 100 hg38.150200.bed.split19084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19085 0 1 2 100 hg38.150200.bed.split19085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19086 0 1 2 100 hg38.150200.bed.split19086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19087 0 1 2 100 hg38.150200.bed.split19087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19088 0 1 2 100 hg38.150200.bed.split19088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19089 0 1 2 100 hg38.150200.bed.split19089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1909 0 1 2 100 hg38.150200.bed.split1909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19090 0 1 2 100 hg38.150200.bed.split19090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19091 0 1 2 100 hg38.150200.bed.split19091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19092 0 1 2 100 hg38.150200.bed.split19092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19093 0 1 2 100 hg38.150200.bed.split19093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19094 0 1 2 100 hg38.150200.bed.split19094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19095 0 1 2 100 hg38.150200.bed.split19095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19096 0 1 2 100 hg38.150200.bed.split19096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19097 0 1 2 100 hg38.150200.bed.split19097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19098 0 1 2 100 hg38.150200.bed.split19098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19099 0 1 2 100 hg38.150200.bed.split19099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split191 0 1 2 100 hg38.150200.bed.split191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1910 0 1 2 100 hg38.150200.bed.split1910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19100 0 1 2 100 hg38.150200.bed.split19100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19101 0 1 2 100 hg38.150200.bed.split19101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19102 0 1 2 100 hg38.150200.bed.split19102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19103 0 1 2 100 hg38.150200.bed.split19103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19104 0 1 2 100 hg38.150200.bed.split19104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19105 0 1 2 100 hg38.150200.bed.split19105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19106 0 1 2 100 hg38.150200.bed.split19106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19107 0 1 2 100 hg38.150200.bed.split19107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19108 0 1 2 100 hg38.150200.bed.split19108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19109 0 1 2 100 hg38.150200.bed.split19109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1911 0 1 2 100 hg38.150200.bed.split1911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19110 0 1 2 100 hg38.150200.bed.split19110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19111 0 1 2 100 hg38.150200.bed.split19111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19112 0 1 2 100 hg38.150200.bed.split19112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19113 0 1 2 100 hg38.150200.bed.split19113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19114 0 1 2 100 hg38.150200.bed.split19114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19115 0 1 2 100 hg38.150200.bed.split19115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19116 0 1 2 100 hg38.150200.bed.split19116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19117 0 1 2 100 hg38.150200.bed.split19117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19118 0 1 2 100 hg38.150200.bed.split19118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19119 0 1 2 100 hg38.150200.bed.split19119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1912 0 1 2 100 hg38.150200.bed.split1912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19120 0 1 2 100 hg38.150200.bed.split19120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19121 0 1 2 100 hg38.150200.bed.split19121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19122 0 1 2 100 hg38.150200.bed.split19122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19123 0 1 2 100 hg38.150200.bed.split19123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19124 0 1 2 100 hg38.150200.bed.split19124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19125 0 1 2 100 hg38.150200.bed.split19125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19126 0 1 2 100 hg38.150200.bed.split19126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19127 0 1 2 100 hg38.150200.bed.split19127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19128 0 1 2 100 hg38.150200.bed.split19128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19129 0 1 2 100 hg38.150200.bed.split19129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1913 0 1 2 100 hg38.150200.bed.split1913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19130 0 1 2 100 hg38.150200.bed.split19130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19131 0 1 2 100 hg38.150200.bed.split19131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19132 0 1 2 100 hg38.150200.bed.split19132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19133 0 1 2 100 hg38.150200.bed.split19133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19134 0 1 2 100 hg38.150200.bed.split19134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19135 0 1 2 100 hg38.150200.bed.split19135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19136 0 1 2 100 hg38.150200.bed.split19136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19137 0 1 2 100 hg38.150200.bed.split19137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19138 0 1 2 100 hg38.150200.bed.split19138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19139 0 1 2 100 hg38.150200.bed.split19139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1914 0 1 2 100 hg38.150200.bed.split1914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19140 0 1 2 100 hg38.150200.bed.split19140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19141 0 1 2 100 hg38.150200.bed.split19141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19142 0 1 2 100 hg38.150200.bed.split19142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19143 0 1 2 100 hg38.150200.bed.split19143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19144 0 1 2 100 hg38.150200.bed.split19144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19145 0 1 2 100 hg38.150200.bed.split19145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19146 0 1 2 100 hg38.150200.bed.split19146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19147 0 1 2 100 hg38.150200.bed.split19147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19148 0 1 2 100 hg38.150200.bed.split19148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19149 0 1 2 100 hg38.150200.bed.split19149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1915 0 1 2 100 hg38.150200.bed.split1915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19150 0 1 2 100 hg38.150200.bed.split19150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19151 0 1 2 100 hg38.150200.bed.split19151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19152 0 1 2 100 hg38.150200.bed.split19152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19153 0 1 2 100 hg38.150200.bed.split19153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19154 0 1 2 100 hg38.150200.bed.split19154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19155 0 1 2 100 hg38.150200.bed.split19155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19156 0 1 2 100 hg38.150200.bed.split19156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19157 0 1 2 100 hg38.150200.bed.split19157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19158 0 1 2 100 hg38.150200.bed.split19158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19159 0 1 2 100 hg38.150200.bed.split19159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1916 0 1 2 100 hg38.150200.bed.split1916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19160 0 1 2 100 hg38.150200.bed.split19160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19161 0 1 2 100 hg38.150200.bed.split19161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19162 0 1 2 100 hg38.150200.bed.split19162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19163 0 1 2 100 hg38.150200.bed.split19163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19164 0 1 2 100 hg38.150200.bed.split19164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19165 0 1 2 100 hg38.150200.bed.split19165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19166 0 1 2 100 hg38.150200.bed.split19166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19167 0 1 2 100 hg38.150200.bed.split19167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19168 0 1 2 100 hg38.150200.bed.split19168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19169 0 1 2 100 hg38.150200.bed.split19169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1917 0 1 2 100 hg38.150200.bed.split1917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19170 0 1 2 100 hg38.150200.bed.split19170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19171 0 1 2 100 hg38.150200.bed.split19171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19172 0 1 2 100 hg38.150200.bed.split19172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19173 0 1 2 100 hg38.150200.bed.split19173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19174 0 1 2 100 hg38.150200.bed.split19174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19175 0 1 2 100 hg38.150200.bed.split19175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19176 0 1 2 100 hg38.150200.bed.split19176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19177 0 1 2 100 hg38.150200.bed.split19177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19178 0 1 2 100 hg38.150200.bed.split19178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19179 0 1 2 100 hg38.150200.bed.split19179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1918 0 1 2 100 hg38.150200.bed.split1918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19180 0 1 2 100 hg38.150200.bed.split19180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19181 0 1 2 100 hg38.150200.bed.split19181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19182 0 1 2 100 hg38.150200.bed.split19182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19183 0 1 2 100 hg38.150200.bed.split19183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19184 0 1 2 100 hg38.150200.bed.split19184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19185 0 1 2 100 hg38.150200.bed.split19185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19186 0 1 2 100 hg38.150200.bed.split19186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19187 0 1 2 100 hg38.150200.bed.split19187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19188 0 1 2 100 hg38.150200.bed.split19188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19189 0 1 2 100 hg38.150200.bed.split19189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1919 0 1 2 100 hg38.150200.bed.split1919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19190 0 1 2 100 hg38.150200.bed.split19190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19191 0 1 2 100 hg38.150200.bed.split19191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19192 0 1 2 100 hg38.150200.bed.split19192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19193 0 1 2 100 hg38.150200.bed.split19193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19194 0 1 2 100 hg38.150200.bed.split19194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19195 0 1 2 100 hg38.150200.bed.split19195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19196 0 1 2 100 hg38.150200.bed.split19196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19197 0 1 2 100 hg38.150200.bed.split19197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19198 0 1 2 100 hg38.150200.bed.split19198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19199 0 1 2 100 hg38.150200.bed.split19199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split192 0 1 2 100 hg38.150200.bed.split192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1920 0 1 2 100 hg38.150200.bed.split1920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19200 0 1 2 100 hg38.150200.bed.split19200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19201 0 1 2 100 hg38.150200.bed.split19201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19202 0 1 2 100 hg38.150200.bed.split19202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19203 0 1 2 100 hg38.150200.bed.split19203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19204 0 1 2 100 hg38.150200.bed.split19204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19205 0 1 2 100 hg38.150200.bed.split19205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19206 0 1 2 100 hg38.150200.bed.split19206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19207 0 1 2 100 hg38.150200.bed.split19207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19208 0 1 2 100 hg38.150200.bed.split19208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19209 0 1 2 100 hg38.150200.bed.split19209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1921 0 1 2 100 hg38.150200.bed.split1921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19210 0 1 2 100 hg38.150200.bed.split19210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19211 0 1 2 100 hg38.150200.bed.split19211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19212 0 1 2 100 hg38.150200.bed.split19212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19213 0 1 2 100 hg38.150200.bed.split19213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19214 0 1 2 100 hg38.150200.bed.split19214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19215 0 1 2 100 hg38.150200.bed.split19215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19216 0 1 2 100 hg38.150200.bed.split19216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19217 0 1 2 100 hg38.150200.bed.split19217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19218 0 1 2 100 hg38.150200.bed.split19218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19219 0 1 2 100 hg38.150200.bed.split19219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1922 0 1 2 100 hg38.150200.bed.split1922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19220 0 1 2 100 hg38.150200.bed.split19220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19221 0 1 2 100 hg38.150200.bed.split19221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19222 0 1 2 100 hg38.150200.bed.split19222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19223 0 1 2 100 hg38.150200.bed.split19223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19224 0 1 2 100 hg38.150200.bed.split19224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19225 0 1 2 100 hg38.150200.bed.split19225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19226 0 1 2 100 hg38.150200.bed.split19226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19227 0 1 2 100 hg38.150200.bed.split19227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19228 0 1 2 100 hg38.150200.bed.split19228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19229 0 1 2 100 hg38.150200.bed.split19229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1923 0 1 2 100 hg38.150200.bed.split1923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19230 0 1 2 100 hg38.150200.bed.split19230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19231 0 1 2 100 hg38.150200.bed.split19231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19232 0 1 2 100 hg38.150200.bed.split19232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19233 0 1 2 100 hg38.150200.bed.split19233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19234 0 1 2 100 hg38.150200.bed.split19234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19235 0 1 2 100 hg38.150200.bed.split19235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19236 0 1 2 100 hg38.150200.bed.split19236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19237 0 1 2 100 hg38.150200.bed.split19237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19238 0 1 2 100 hg38.150200.bed.split19238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19239 0 1 2 100 hg38.150200.bed.split19239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1924 0 1 2 100 hg38.150200.bed.split1924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19240 0 1 2 100 hg38.150200.bed.split19240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19241 0 1 2 100 hg38.150200.bed.split19241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19242 0 1 2 100 hg38.150200.bed.split19242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19243 0 1 2 100 hg38.150200.bed.split19243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19244 0 1 2 100 hg38.150200.bed.split19244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19245 0 1 2 100 hg38.150200.bed.split19245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19246 0 1 2 100 hg38.150200.bed.split19246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19247 0 1 2 100 hg38.150200.bed.split19247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19248 0 1 2 100 hg38.150200.bed.split19248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19249 0 1 2 100 hg38.150200.bed.split19249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1925 0 1 2 100 hg38.150200.bed.split1925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19250 0 1 2 100 hg38.150200.bed.split19250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19251 0 1 2 100 hg38.150200.bed.split19251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19252 0 1 2 100 hg38.150200.bed.split19252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19253 0 1 2 100 hg38.150200.bed.split19253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19254 0 1 2 100 hg38.150200.bed.split19254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19255 0 1 2 100 hg38.150200.bed.split19255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19256 0 1 2 100 hg38.150200.bed.split19256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19257 0 1 2 100 hg38.150200.bed.split19257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19258 0 1 2 100 hg38.150200.bed.split19258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19259 0 1 2 100 hg38.150200.bed.split19259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1926 0 1 2 100 hg38.150200.bed.split1926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19260 0 1 2 100 hg38.150200.bed.split19260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19261 0 1 2 100 hg38.150200.bed.split19261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19262 0 1 2 100 hg38.150200.bed.split19262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19263 0 1 2 100 hg38.150200.bed.split19263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19264 0 1 2 100 hg38.150200.bed.split19264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19265 0 1 2 100 hg38.150200.bed.split19265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19266 0 1 2 100 hg38.150200.bed.split19266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19267 0 1 2 100 hg38.150200.bed.split19267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19268 0 1 2 100 hg38.150200.bed.split19268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19269 0 1 2 100 hg38.150200.bed.split19269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1927 0 1 2 100 hg38.150200.bed.split1927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19270 0 1 2 100 hg38.150200.bed.split19270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19271 0 1 2 100 hg38.150200.bed.split19271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19272 0 1 2 100 hg38.150200.bed.split19272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19273 0 1 2 100 hg38.150200.bed.split19273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19274 0 1 2 100 hg38.150200.bed.split19274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19275 0 1 2 100 hg38.150200.bed.split19275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19276 0 1 2 100 hg38.150200.bed.split19276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19277 0 1 2 100 hg38.150200.bed.split19277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19278 0 1 2 100 hg38.150200.bed.split19278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19279 0 1 2 100 hg38.150200.bed.split19279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1928 0 1 2 100 hg38.150200.bed.split1928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19280 0 1 2 100 hg38.150200.bed.split19280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19281 0 1 2 100 hg38.150200.bed.split19281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19282 0 1 2 100 hg38.150200.bed.split19282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19283 0 1 2 100 hg38.150200.bed.split19283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19284 0 1 2 100 hg38.150200.bed.split19284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19285 0 1 2 100 hg38.150200.bed.split19285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19286 0 1 2 100 hg38.150200.bed.split19286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19287 0 1 2 100 hg38.150200.bed.split19287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19288 0 1 2 100 hg38.150200.bed.split19288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19289 0 1 2 100 hg38.150200.bed.split19289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1929 0 1 2 100 hg38.150200.bed.split1929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19290 0 1 2 100 hg38.150200.bed.split19290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19291 0 1 2 100 hg38.150200.bed.split19291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19292 0 1 2 100 hg38.150200.bed.split19292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19293 0 1 2 100 hg38.150200.bed.split19293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19294 0 1 2 100 hg38.150200.bed.split19294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19295 0 1 2 100 hg38.150200.bed.split19295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19296 0 1 2 100 hg38.150200.bed.split19296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19297 0 1 2 100 hg38.150200.bed.split19297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19298 0 1 2 100 hg38.150200.bed.split19298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19299 0 1 2 100 hg38.150200.bed.split19299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split193 0 1 2 100 hg38.150200.bed.split193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1930 0 1 2 100 hg38.150200.bed.split1930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19300 0 1 2 100 hg38.150200.bed.split19300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19301 0 1 2 100 hg38.150200.bed.split19301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19302 0 1 2 100 hg38.150200.bed.split19302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19303 0 1 2 100 hg38.150200.bed.split19303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19304 0 1 2 100 hg38.150200.bed.split19304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19305 0 1 2 100 hg38.150200.bed.split19305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19306 0 1 2 100 hg38.150200.bed.split19306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19307 0 1 2 100 hg38.150200.bed.split19307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19308 0 1 2 100 hg38.150200.bed.split19308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19309 0 1 2 100 hg38.150200.bed.split19309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1931 0 1 2 100 hg38.150200.bed.split1931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19310 0 1 2 100 hg38.150200.bed.split19310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19311 0 1 2 100 hg38.150200.bed.split19311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19312 0 1 2 100 hg38.150200.bed.split19312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19313 0 1 2 100 hg38.150200.bed.split19313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19314 0 1 2 100 hg38.150200.bed.split19314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19315 0 1 2 100 hg38.150200.bed.split19315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19316 0 1 2 100 hg38.150200.bed.split19316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19317 0 1 2 100 hg38.150200.bed.split19317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19318 0 1 2 100 hg38.150200.bed.split19318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19319 0 1 2 100 hg38.150200.bed.split19319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1932 0 1 2 100 hg38.150200.bed.split1932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19320 0 1 2 100 hg38.150200.bed.split19320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19321 0 1 2 100 hg38.150200.bed.split19321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19322 0 1 2 100 hg38.150200.bed.split19322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19323 0 1 2 100 hg38.150200.bed.split19323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19324 0 1 2 100 hg38.150200.bed.split19324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19325 0 1 2 100 hg38.150200.bed.split19325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19326 0 1 2 100 hg38.150200.bed.split19326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19327 0 1 2 100 hg38.150200.bed.split19327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19328 0 1 2 100 hg38.150200.bed.split19328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19329 0 1 2 100 hg38.150200.bed.split19329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1933 0 1 2 100 hg38.150200.bed.split1933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19330 0 1 2 100 hg38.150200.bed.split19330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19331 0 1 2 100 hg38.150200.bed.split19331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19332 0 1 2 100 hg38.150200.bed.split19332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19333 0 1 2 100 hg38.150200.bed.split19333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19334 0 1 2 100 hg38.150200.bed.split19334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19335 0 1 2 100 hg38.150200.bed.split19335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19336 0 1 2 100 hg38.150200.bed.split19336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19337 0 1 2 100 hg38.150200.bed.split19337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19338 0 1 2 100 hg38.150200.bed.split19338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19339 0 1 2 100 hg38.150200.bed.split19339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1934 0 1 2 100 hg38.150200.bed.split1934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19340 0 1 2 100 hg38.150200.bed.split19340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19341 0 1 2 100 hg38.150200.bed.split19341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19342 0 1 2 100 hg38.150200.bed.split19342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19343 0 1 2 100 hg38.150200.bed.split19343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19344 0 1 2 100 hg38.150200.bed.split19344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19345 0 1 2 100 hg38.150200.bed.split19345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19346 0 1 2 100 hg38.150200.bed.split19346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19347 0 1 2 100 hg38.150200.bed.split19347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19348 0 1 2 100 hg38.150200.bed.split19348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19349 0 1 2 100 hg38.150200.bed.split19349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1935 0 1 2 100 hg38.150200.bed.split1935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19350 0 1 2 100 hg38.150200.bed.split19350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19351 0 1 2 100 hg38.150200.bed.split19351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19352 0 1 2 100 hg38.150200.bed.split19352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19353 0 1 2 100 hg38.150200.bed.split19353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19354 0 1 2 100 hg38.150200.bed.split19354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19355 0 1 2 100 hg38.150200.bed.split19355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19356 0 1 2 100 hg38.150200.bed.split19356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19357 0 1 2 100 hg38.150200.bed.split19357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19358 0 1 2 100 hg38.150200.bed.split19358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19359 0 1 2 100 hg38.150200.bed.split19359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1936 0 1 2 100 hg38.150200.bed.split1936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19360 0 1 2 100 hg38.150200.bed.split19360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19361 0 1 2 100 hg38.150200.bed.split19361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19362 0 1 2 100 hg38.150200.bed.split19362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19363 0 1 2 100 hg38.150200.bed.split19363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19364 0 1 2 100 hg38.150200.bed.split19364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19365 0 1 2 100 hg38.150200.bed.split19365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19366 0 1 2 100 hg38.150200.bed.split19366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19367 0 1 2 100 hg38.150200.bed.split19367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19368 0 1 2 100 hg38.150200.bed.split19368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19369 0 1 2 100 hg38.150200.bed.split19369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1937 0 1 2 100 hg38.150200.bed.split1937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19370 0 1 2 100 hg38.150200.bed.split19370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19371 0 1 2 100 hg38.150200.bed.split19371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19372 0 1 2 100 hg38.150200.bed.split19372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19373 0 1 2 100 hg38.150200.bed.split19373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19374 0 1 2 100 hg38.150200.bed.split19374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19375 0 1 2 100 hg38.150200.bed.split19375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19376 0 1 2 100 hg38.150200.bed.split19376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19377 0 1 2 100 hg38.150200.bed.split19377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19378 0 1 2 100 hg38.150200.bed.split19378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19379 0 1 2 100 hg38.150200.bed.split19379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1938 0 1 2 100 hg38.150200.bed.split1938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19380 0 1 2 100 hg38.150200.bed.split19380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19381 0 1 2 100 hg38.150200.bed.split19381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19382 0 1 2 100 hg38.150200.bed.split19382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19383 0 1 2 100 hg38.150200.bed.split19383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19384 0 1 2 100 hg38.150200.bed.split19384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19385 0 1 2 100 hg38.150200.bed.split19385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19386 0 1 2 100 hg38.150200.bed.split19386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19387 0 1 2 100 hg38.150200.bed.split19387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19388 0 1 2 100 hg38.150200.bed.split19388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19389 0 1 2 100 hg38.150200.bed.split19389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1939 0 1 2 100 hg38.150200.bed.split1939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19390 0 1 2 100 hg38.150200.bed.split19390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19391 0 1 2 100 hg38.150200.bed.split19391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19392 0 1 2 100 hg38.150200.bed.split19392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19393 0 1 2 100 hg38.150200.bed.split19393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19394 0 1 2 100 hg38.150200.bed.split19394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19395 0 1 2 100 hg38.150200.bed.split19395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19396 0 1 2 100 hg38.150200.bed.split19396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19397 0 1 2 100 hg38.150200.bed.split19397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19398 0 1 2 100 hg38.150200.bed.split19398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19399 0 1 2 100 hg38.150200.bed.split19399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split194 0 1 2 100 hg38.150200.bed.split194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1940 0 1 2 100 hg38.150200.bed.split1940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19400 0 1 2 100 hg38.150200.bed.split19400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19401 0 1 2 100 hg38.150200.bed.split19401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19402 0 1 2 100 hg38.150200.bed.split19402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19403 0 1 2 100 hg38.150200.bed.split19403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19404 0 1 2 100 hg38.150200.bed.split19404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19405 0 1 2 100 hg38.150200.bed.split19405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19406 0 1 2 100 hg38.150200.bed.split19406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19407 0 1 2 100 hg38.150200.bed.split19407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19408 0 1 2 100 hg38.150200.bed.split19408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19409 0 1 2 100 hg38.150200.bed.split19409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1941 0 1 2 100 hg38.150200.bed.split1941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19410 0 1 2 100 hg38.150200.bed.split19410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19411 0 1 2 100 hg38.150200.bed.split19411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19412 0 1 2 100 hg38.150200.bed.split19412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19413 0 1 2 100 hg38.150200.bed.split19413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19414 0 1 2 100 hg38.150200.bed.split19414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19415 0 1 2 100 hg38.150200.bed.split19415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19416 0 1 2 100 hg38.150200.bed.split19416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19417 0 1 2 100 hg38.150200.bed.split19417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19418 0 1 2 100 hg38.150200.bed.split19418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19419 0 1 2 100 hg38.150200.bed.split19419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1942 0 1 2 100 hg38.150200.bed.split1942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19420 0 1 2 100 hg38.150200.bed.split19420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19421 0 1 2 100 hg38.150200.bed.split19421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19422 0 1 2 100 hg38.150200.bed.split19422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19423 0 1 2 100 hg38.150200.bed.split19423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19424 0 1 2 100 hg38.150200.bed.split19424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19425 0 1 2 100 hg38.150200.bed.split19425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19426 0 1 2 100 hg38.150200.bed.split19426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19427 0 1 2 100 hg38.150200.bed.split19427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19428 0 1 2 100 hg38.150200.bed.split19428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19429 0 1 2 100 hg38.150200.bed.split19429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1943 0 1 2 100 hg38.150200.bed.split1943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19430 0 1 2 100 hg38.150200.bed.split19430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19431 0 1 2 100 hg38.150200.bed.split19431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19432 0 1 2 100 hg38.150200.bed.split19432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19433 0 1 2 100 hg38.150200.bed.split19433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19434 0 1 2 100 hg38.150200.bed.split19434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19435 0 1 2 100 hg38.150200.bed.split19435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19436 0 1 2 100 hg38.150200.bed.split19436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19437 0 1 2 100 hg38.150200.bed.split19437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19438 0 1 2 100 hg38.150200.bed.split19438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19439 0 1 2 100 hg38.150200.bed.split19439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1944 0 1 2 100 hg38.150200.bed.split1944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19440 0 1 2 100 hg38.150200.bed.split19440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19441 0 1 2 100 hg38.150200.bed.split19441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19442 0 1 2 100 hg38.150200.bed.split19442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19443 0 1 2 100 hg38.150200.bed.split19443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19444 0 1 2 100 hg38.150200.bed.split19444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19445 0 1 2 100 hg38.150200.bed.split19445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19446 0 1 2 100 hg38.150200.bed.split19446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19447 0 1 2 100 hg38.150200.bed.split19447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19448 0 1 2 100 hg38.150200.bed.split19448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19449 0 1 2 100 hg38.150200.bed.split19449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1945 0 1 2 100 hg38.150200.bed.split1945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19450 0 1 2 100 hg38.150200.bed.split19450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19451 0 1 2 100 hg38.150200.bed.split19451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19452 0 1 2 100 hg38.150200.bed.split19452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19453 0 1 2 100 hg38.150200.bed.split19453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19454 0 1 2 100 hg38.150200.bed.split19454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19455 0 1 2 100 hg38.150200.bed.split19455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19456 0 1 2 100 hg38.150200.bed.split19456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19457 0 1 2 100 hg38.150200.bed.split19457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19458 0 1 2 100 hg38.150200.bed.split19458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19459 0 1 2 100 hg38.150200.bed.split19459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1946 0 1 2 100 hg38.150200.bed.split1946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19460 0 1 2 100 hg38.150200.bed.split19460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19461 0 1 2 100 hg38.150200.bed.split19461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19462 0 1 2 100 hg38.150200.bed.split19462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19463 0 1 2 100 hg38.150200.bed.split19463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19464 0 1 2 100 hg38.150200.bed.split19464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19465 0 1 2 100 hg38.150200.bed.split19465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19466 0 1 2 100 hg38.150200.bed.split19466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19467 0 1 2 100 hg38.150200.bed.split19467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19468 0 1 2 100 hg38.150200.bed.split19468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19469 0 1 2 100 hg38.150200.bed.split19469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1947 0 1 2 100 hg38.150200.bed.split1947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19470 0 1 2 100 hg38.150200.bed.split19470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19471 0 1 2 100 hg38.150200.bed.split19471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19472 0 1 2 100 hg38.150200.bed.split19472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19473 0 1 2 100 hg38.150200.bed.split19473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19474 0 1 2 100 hg38.150200.bed.split19474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19475 0 1 2 100 hg38.150200.bed.split19475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19476 0 1 2 100 hg38.150200.bed.split19476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19477 0 1 2 100 hg38.150200.bed.split19477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19478 0 1 2 100 hg38.150200.bed.split19478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19479 0 1 2 100 hg38.150200.bed.split19479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1948 0 1 2 100 hg38.150200.bed.split1948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19480 0 1 2 100 hg38.150200.bed.split19480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19481 0 1 2 100 hg38.150200.bed.split19481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19482 0 1 2 100 hg38.150200.bed.split19482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19483 0 1 2 100 hg38.150200.bed.split19483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19484 0 1 2 100 hg38.150200.bed.split19484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19485 0 1 2 100 hg38.150200.bed.split19485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19486 0 1 2 100 hg38.150200.bed.split19486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19487 0 1 2 100 hg38.150200.bed.split19487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19488 0 1 2 100 hg38.150200.bed.split19488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19489 0 1 2 100 hg38.150200.bed.split19489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1949 0 1 2 100 hg38.150200.bed.split1949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19490 0 1 2 100 hg38.150200.bed.split19490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19491 0 1 2 100 hg38.150200.bed.split19491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19492 0 1 2 100 hg38.150200.bed.split19492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19493 0 1 2 100 hg38.150200.bed.split19493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19494 0 1 2 100 hg38.150200.bed.split19494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19495 0 1 2 100 hg38.150200.bed.split19495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19496 0 1 2 100 hg38.150200.bed.split19496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19497 0 1 2 100 hg38.150200.bed.split19497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19498 0 1 2 100 hg38.150200.bed.split19498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19499 0 1 2 100 hg38.150200.bed.split19499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split195 0 1 2 100 hg38.150200.bed.split195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1950 0 1 2 100 hg38.150200.bed.split1950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19500 0 1 2 100 hg38.150200.bed.split19500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19501 0 1 2 100 hg38.150200.bed.split19501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19502 0 1 2 100 hg38.150200.bed.split19502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19503 0 1 2 100 hg38.150200.bed.split19503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19504 0 1 2 100 hg38.150200.bed.split19504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19505 0 1 2 100 hg38.150200.bed.split19505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19506 0 1 2 100 hg38.150200.bed.split19506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19507 0 1 2 100 hg38.150200.bed.split19507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19508 0 1 2 100 hg38.150200.bed.split19508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19509 0 1 2 100 hg38.150200.bed.split19509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1951 0 1 2 100 hg38.150200.bed.split1951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19510 0 1 2 100 hg38.150200.bed.split19510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19511 0 1 2 100 hg38.150200.bed.split19511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19512 0 1 2 100 hg38.150200.bed.split19512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19513 0 1 2 100 hg38.150200.bed.split19513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19514 0 1 2 100 hg38.150200.bed.split19514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19515 0 1 2 100 hg38.150200.bed.split19515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19516 0 1 2 100 hg38.150200.bed.split19516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19517 0 1 2 100 hg38.150200.bed.split19517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19518 0 1 2 100 hg38.150200.bed.split19518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19519 0 1 2 100 hg38.150200.bed.split19519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1952 0 1 2 100 hg38.150200.bed.split1952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19520 0 1 2 100 hg38.150200.bed.split19520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19521 0 1 2 100 hg38.150200.bed.split19521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19522 0 1 2 100 hg38.150200.bed.split19522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19523 0 1 2 100 hg38.150200.bed.split19523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19524 0 1 2 100 hg38.150200.bed.split19524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19525 0 1 2 100 hg38.150200.bed.split19525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19526 0 1 2 100 hg38.150200.bed.split19526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19527 0 1 2 100 hg38.150200.bed.split19527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19528 0 1 2 100 hg38.150200.bed.split19528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19529 0 1 2 100 hg38.150200.bed.split19529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1953 0 1 2 100 hg38.150200.bed.split1953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19530 0 1 2 100 hg38.150200.bed.split19530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19531 0 1 2 100 hg38.150200.bed.split19531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19532 0 1 2 100 hg38.150200.bed.split19532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19533 0 1 2 100 hg38.150200.bed.split19533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19534 0 1 2 100 hg38.150200.bed.split19534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19535 0 1 2 100 hg38.150200.bed.split19535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19536 0 1 2 100 hg38.150200.bed.split19536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19537 0 1 2 100 hg38.150200.bed.split19537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19538 0 1 2 100 hg38.150200.bed.split19538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19539 0 1 2 100 hg38.150200.bed.split19539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1954 0 1 2 100 hg38.150200.bed.split1954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19540 0 1 2 100 hg38.150200.bed.split19540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19541 0 1 2 100 hg38.150200.bed.split19541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19542 0 1 2 100 hg38.150200.bed.split19542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19543 0 1 2 100 hg38.150200.bed.split19543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19544 0 1 2 100 hg38.150200.bed.split19544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19545 0 1 2 100 hg38.150200.bed.split19545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19546 0 1 2 100 hg38.150200.bed.split19546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19547 0 1 2 100 hg38.150200.bed.split19547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19548 0 1 2 100 hg38.150200.bed.split19548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19549 0 1 2 100 hg38.150200.bed.split19549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1955 0 1 2 100 hg38.150200.bed.split1955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19550 0 1 2 100 hg38.150200.bed.split19550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19551 0 1 2 100 hg38.150200.bed.split19551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19552 0 1 2 100 hg38.150200.bed.split19552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19553 0 1 2 100 hg38.150200.bed.split19553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19554 0 1 2 100 hg38.150200.bed.split19554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19555 0 1 2 100 hg38.150200.bed.split19555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19556 0 1 2 100 hg38.150200.bed.split19556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19557 0 1 2 100 hg38.150200.bed.split19557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19558 0 1 2 100 hg38.150200.bed.split19558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19559 0 1 2 100 hg38.150200.bed.split19559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1956 0 1 2 100 hg38.150200.bed.split1956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19560 0 1 2 100 hg38.150200.bed.split19560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19561 0 1 2 100 hg38.150200.bed.split19561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19562 0 1 2 100 hg38.150200.bed.split19562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19563 0 1 2 100 hg38.150200.bed.split19563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19564 0 1 2 100 hg38.150200.bed.split19564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19565 0 1 2 100 hg38.150200.bed.split19565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19566 0 1 2 100 hg38.150200.bed.split19566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19567 0 1 2 100 hg38.150200.bed.split19567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19568 0 1 2 100 hg38.150200.bed.split19568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19569 0 1 2 100 hg38.150200.bed.split19569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1957 0 1 2 100 hg38.150200.bed.split1957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19570 0 1 2 100 hg38.150200.bed.split19570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19571 0 1 2 100 hg38.150200.bed.split19571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19572 0 1 2 100 hg38.150200.bed.split19572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19573 0 1 2 100 hg38.150200.bed.split19573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19574 0 1 2 100 hg38.150200.bed.split19574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19575 0 1 2 100 hg38.150200.bed.split19575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19576 0 1 2 100 hg38.150200.bed.split19576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19577 0 1 2 100 hg38.150200.bed.split19577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19578 0 1 2 100 hg38.150200.bed.split19578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19579 0 1 2 100 hg38.150200.bed.split19579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1958 0 1 2 100 hg38.150200.bed.split1958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19580 0 1 2 100 hg38.150200.bed.split19580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19581 0 1 2 100 hg38.150200.bed.split19581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19582 0 1 2 100 hg38.150200.bed.split19582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19583 0 1 2 100 hg38.150200.bed.split19583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19584 0 1 2 100 hg38.150200.bed.split19584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19585 0 1 2 100 hg38.150200.bed.split19585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19586 0 1 2 100 hg38.150200.bed.split19586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19587 0 1 2 100 hg38.150200.bed.split19587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19588 0 1 2 100 hg38.150200.bed.split19588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19589 0 1 2 100 hg38.150200.bed.split19589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1959 0 1 2 100 hg38.150200.bed.split1959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19590 0 1 2 100 hg38.150200.bed.split19590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19591 0 1 2 100 hg38.150200.bed.split19591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19592 0 1 2 100 hg38.150200.bed.split19592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19593 0 1 2 100 hg38.150200.bed.split19593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19594 0 1 2 100 hg38.150200.bed.split19594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19595 0 1 2 100 hg38.150200.bed.split19595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19596 0 1 2 100 hg38.150200.bed.split19596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19597 0 1 2 100 hg38.150200.bed.split19597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19598 0 1 2 100 hg38.150200.bed.split19598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19599 0 1 2 100 hg38.150200.bed.split19599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split196 0 1 2 100 hg38.150200.bed.split196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1960 0 1 2 100 hg38.150200.bed.split1960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19600 0 1 2 100 hg38.150200.bed.split19600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19601 0 1 2 100 hg38.150200.bed.split19601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19602 0 1 2 100 hg38.150200.bed.split19602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19603 0 1 2 100 hg38.150200.bed.split19603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19604 0 1 2 100 hg38.150200.bed.split19604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19605 0 1 2 100 hg38.150200.bed.split19605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19606 0 1 2 100 hg38.150200.bed.split19606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19607 0 1 2 100 hg38.150200.bed.split19607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19608 0 1 2 100 hg38.150200.bed.split19608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19609 0 1 2 100 hg38.150200.bed.split19609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1961 0 1 2 100 hg38.150200.bed.split1961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19610 0 1 2 100 hg38.150200.bed.split19610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19611 0 1 2 100 hg38.150200.bed.split19611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19612 0 1 2 100 hg38.150200.bed.split19612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19613 0 1 2 100 hg38.150200.bed.split19613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19614 0 1 2 100 hg38.150200.bed.split19614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19615 0 1 2 100 hg38.150200.bed.split19615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19616 0 1 2 100 hg38.150200.bed.split19616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19617 0 1 2 100 hg38.150200.bed.split19617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19618 0 1 2 100 hg38.150200.bed.split19618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19619 0 1 2 100 hg38.150200.bed.split19619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1962 0 1 2 100 hg38.150200.bed.split1962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19620 0 1 2 100 hg38.150200.bed.split19620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19621 0 1 2 100 hg38.150200.bed.split19621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19622 0 1 2 100 hg38.150200.bed.split19622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19623 0 1 2 100 hg38.150200.bed.split19623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19624 0 1 2 100 hg38.150200.bed.split19624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19625 0 1 2 100 hg38.150200.bed.split19625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19626 0 1 2 100 hg38.150200.bed.split19626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19627 0 1 2 100 hg38.150200.bed.split19627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19628 0 1 2 100 hg38.150200.bed.split19628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19629 0 1 2 100 hg38.150200.bed.split19629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1963 0 1 2 100 hg38.150200.bed.split1963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19630 0 1 2 100 hg38.150200.bed.split19630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19631 0 1 2 100 hg38.150200.bed.split19631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19632 0 1 2 100 hg38.150200.bed.split19632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19633 0 1 2 100 hg38.150200.bed.split19633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19634 0 1 2 100 hg38.150200.bed.split19634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19635 0 1 2 100 hg38.150200.bed.split19635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19636 0 1 2 100 hg38.150200.bed.split19636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19637 0 1 2 100 hg38.150200.bed.split19637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19638 0 1 2 100 hg38.150200.bed.split19638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19639 0 1 2 100 hg38.150200.bed.split19639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1964 0 1 2 100 hg38.150200.bed.split1964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19640 0 1 2 100 hg38.150200.bed.split19640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19641 0 1 2 100 hg38.150200.bed.split19641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19642 0 1 2 100 hg38.150200.bed.split19642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19643 0 1 2 100 hg38.150200.bed.split19643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19644 0 1 2 100 hg38.150200.bed.split19644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19645 0 1 2 100 hg38.150200.bed.split19645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19646 0 1 2 100 hg38.150200.bed.split19646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19647 0 1 2 100 hg38.150200.bed.split19647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19648 0 1 2 100 hg38.150200.bed.split19648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19649 0 1 2 100 hg38.150200.bed.split19649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1965 0 1 2 100 hg38.150200.bed.split1965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19650 0 1 2 100 hg38.150200.bed.split19650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19651 0 1 2 100 hg38.150200.bed.split19651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19652 0 1 2 100 hg38.150200.bed.split19652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19653 0 1 2 100 hg38.150200.bed.split19653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19654 0 1 2 100 hg38.150200.bed.split19654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19655 0 1 2 100 hg38.150200.bed.split19655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19656 0 1 2 100 hg38.150200.bed.split19656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19657 0 1 2 100 hg38.150200.bed.split19657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19658 0 1 2 100 hg38.150200.bed.split19658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19659 0 1 2 100 hg38.150200.bed.split19659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1966 0 1 2 100 hg38.150200.bed.split1966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19660 0 1 2 100 hg38.150200.bed.split19660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19661 0 1 2 100 hg38.150200.bed.split19661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19662 0 1 2 100 hg38.150200.bed.split19662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19663 0 1 2 100 hg38.150200.bed.split19663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19664 0 1 2 100 hg38.150200.bed.split19664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19665 0 1 2 100 hg38.150200.bed.split19665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19666 0 1 2 100 hg38.150200.bed.split19666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19667 0 1 2 100 hg38.150200.bed.split19667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19668 0 1 2 100 hg38.150200.bed.split19668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19669 0 1 2 100 hg38.150200.bed.split19669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1967 0 1 2 100 hg38.150200.bed.split1967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19670 0 1 2 100 hg38.150200.bed.split19670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19671 0 1 2 100 hg38.150200.bed.split19671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19672 0 1 2 100 hg38.150200.bed.split19672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19673 0 1 2 100 hg38.150200.bed.split19673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19674 0 1 2 100 hg38.150200.bed.split19674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19675 0 1 2 100 hg38.150200.bed.split19675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19676 0 1 2 100 hg38.150200.bed.split19676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19677 0 1 2 100 hg38.150200.bed.split19677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19678 0 1 2 100 hg38.150200.bed.split19678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19679 0 1 2 100 hg38.150200.bed.split19679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1968 0 1 2 100 hg38.150200.bed.split1968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19680 0 1 2 100 hg38.150200.bed.split19680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19681 0 1 2 100 hg38.150200.bed.split19681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19682 0 1 2 100 hg38.150200.bed.split19682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19683 0 1 2 100 hg38.150200.bed.split19683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19684 0 1 2 100 hg38.150200.bed.split19684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19685 0 1 2 100 hg38.150200.bed.split19685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19686 0 1 2 100 hg38.150200.bed.split19686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19687 0 1 2 100 hg38.150200.bed.split19687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19688 0 1 2 100 hg38.150200.bed.split19688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19689 0 1 2 100 hg38.150200.bed.split19689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1969 0 1 2 100 hg38.150200.bed.split1969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19690 0 1 2 100 hg38.150200.bed.split19690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19691 0 1 2 100 hg38.150200.bed.split19691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19692 0 1 2 100 hg38.150200.bed.split19692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19693 0 1 2 100 hg38.150200.bed.split19693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19694 0 1 2 100 hg38.150200.bed.split19694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19695 0 1 2 100 hg38.150200.bed.split19695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19696 0 1 2 100 hg38.150200.bed.split19696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19697 0 1 2 100 hg38.150200.bed.split19697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19698 0 1 2 100 hg38.150200.bed.split19698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19699 0 1 2 100 hg38.150200.bed.split19699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split197 0 1 2 100 hg38.150200.bed.split197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1970 0 1 2 100 hg38.150200.bed.split1970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19700 0 1 2 100 hg38.150200.bed.split19700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19701 0 1 2 100 hg38.150200.bed.split19701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19702 0 1 2 100 hg38.150200.bed.split19702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19703 0 1 2 100 hg38.150200.bed.split19703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19704 0 1 2 100 hg38.150200.bed.split19704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19705 0 1 2 100 hg38.150200.bed.split19705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19706 0 1 2 100 hg38.150200.bed.split19706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19707 0 1 2 100 hg38.150200.bed.split19707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19708 0 1 2 100 hg38.150200.bed.split19708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19709 0 1 2 100 hg38.150200.bed.split19709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1971 0 1 2 100 hg38.150200.bed.split1971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19710 0 1 2 100 hg38.150200.bed.split19710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19711 0 1 2 100 hg38.150200.bed.split19711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19712 0 1 2 100 hg38.150200.bed.split19712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19713 0 1 2 100 hg38.150200.bed.split19713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19714 0 1 2 100 hg38.150200.bed.split19714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19715 0 1 2 100 hg38.150200.bed.split19715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19716 0 1 2 100 hg38.150200.bed.split19716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19717 0 1 2 100 hg38.150200.bed.split19717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19718 0 1 2 100 hg38.150200.bed.split19718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19719 0 1 2 100 hg38.150200.bed.split19719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1972 0 1 2 100 hg38.150200.bed.split1972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19720 0 1 2 100 hg38.150200.bed.split19720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19721 0 1 2 100 hg38.150200.bed.split19721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19722 0 1 2 100 hg38.150200.bed.split19722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19723 0 1 2 100 hg38.150200.bed.split19723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19724 0 1 2 100 hg38.150200.bed.split19724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19725 0 1 2 100 hg38.150200.bed.split19725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19726 0 1 2 100 hg38.150200.bed.split19726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19727 0 1 2 100 hg38.150200.bed.split19727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19728 0 1 2 100 hg38.150200.bed.split19728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19729 0 1 2 100 hg38.150200.bed.split19729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1973 0 1 2 100 hg38.150200.bed.split1973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19730 0 1 2 100 hg38.150200.bed.split19730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19731 0 1 2 100 hg38.150200.bed.split19731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19732 0 1 2 100 hg38.150200.bed.split19732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19733 0 1 2 100 hg38.150200.bed.split19733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19734 0 1 2 100 hg38.150200.bed.split19734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19735 0 1 2 100 hg38.150200.bed.split19735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19736 0 1 2 100 hg38.150200.bed.split19736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19737 0 1 2 100 hg38.150200.bed.split19737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19738 0 1 2 100 hg38.150200.bed.split19738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19739 0 1 2 100 hg38.150200.bed.split19739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1974 0 1 2 100 hg38.150200.bed.split1974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19740 0 1 2 100 hg38.150200.bed.split19740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19741 0 1 2 100 hg38.150200.bed.split19741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19742 0 1 2 100 hg38.150200.bed.split19742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19743 0 1 2 100 hg38.150200.bed.split19743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19744 0 1 2 100 hg38.150200.bed.split19744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19745 0 1 2 100 hg38.150200.bed.split19745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19746 0 1 2 100 hg38.150200.bed.split19746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19747 0 1 2 100 hg38.150200.bed.split19747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19748 0 1 2 100 hg38.150200.bed.split19748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19749 0 1 2 100 hg38.150200.bed.split19749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1975 0 1 2 100 hg38.150200.bed.split1975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19750 0 1 2 100 hg38.150200.bed.split19750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19751 0 1 2 100 hg38.150200.bed.split19751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19752 0 1 2 100 hg38.150200.bed.split19752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19753 0 1 2 100 hg38.150200.bed.split19753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19754 0 1 2 100 hg38.150200.bed.split19754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19755 0 1 2 100 hg38.150200.bed.split19755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19756 0 1 2 100 hg38.150200.bed.split19756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19757 0 1 2 100 hg38.150200.bed.split19757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19758 0 1 2 100 hg38.150200.bed.split19758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19759 0 1 2 100 hg38.150200.bed.split19759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1976 0 1 2 100 hg38.150200.bed.split1976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19760 0 1 2 100 hg38.150200.bed.split19760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19761 0 1 2 100 hg38.150200.bed.split19761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19762 0 1 2 100 hg38.150200.bed.split19762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19763 0 1 2 100 hg38.150200.bed.split19763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19764 0 1 2 100 hg38.150200.bed.split19764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19765 0 1 2 100 hg38.150200.bed.split19765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19766 0 1 2 100 hg38.150200.bed.split19766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19767 0 1 2 100 hg38.150200.bed.split19767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19768 0 1 2 100 hg38.150200.bed.split19768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19769 0 1 2 100 hg38.150200.bed.split19769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1977 0 1 2 100 hg38.150200.bed.split1977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19770 0 1 2 100 hg38.150200.bed.split19770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19771 0 1 2 100 hg38.150200.bed.split19771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19772 0 1 2 100 hg38.150200.bed.split19772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19773 0 1 2 100 hg38.150200.bed.split19773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19774 0 1 2 100 hg38.150200.bed.split19774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19775 0 1 2 100 hg38.150200.bed.split19775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19776 0 1 2 100 hg38.150200.bed.split19776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19777 0 1 2 100 hg38.150200.bed.split19777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19778 0 1 2 100 hg38.150200.bed.split19778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19779 0 1 2 100 hg38.150200.bed.split19779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1978 0 1 2 100 hg38.150200.bed.split1978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19780 0 1 2 100 hg38.150200.bed.split19780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19781 0 1 2 100 hg38.150200.bed.split19781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19782 0 1 2 100 hg38.150200.bed.split19782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19783 0 1 2 100 hg38.150200.bed.split19783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19784 0 1 2 100 hg38.150200.bed.split19784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19785 0 1 2 100 hg38.150200.bed.split19785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19786 0 1 2 100 hg38.150200.bed.split19786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19787 0 1 2 100 hg38.150200.bed.split19787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19788 0 1 2 100 hg38.150200.bed.split19788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19789 0 1 2 100 hg38.150200.bed.split19789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1979 0 1 2 100 hg38.150200.bed.split1979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19790 0 1 2 100 hg38.150200.bed.split19790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19791 0 1 2 100 hg38.150200.bed.split19791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19792 0 1 2 100 hg38.150200.bed.split19792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19793 0 1 2 100 hg38.150200.bed.split19793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19794 0 1 2 100 hg38.150200.bed.split19794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19795 0 1 2 100 hg38.150200.bed.split19795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19796 0 1 2 100 hg38.150200.bed.split19796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19797 0 1 2 100 hg38.150200.bed.split19797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19798 0 1 2 100 hg38.150200.bed.split19798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19799 0 1 2 100 hg38.150200.bed.split19799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split198 0 1 2 100 hg38.150200.bed.split198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1980 0 1 2 100 hg38.150200.bed.split1980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19800 0 1 2 100 hg38.150200.bed.split19800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19801 0 1 2 100 hg38.150200.bed.split19801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19802 0 1 2 100 hg38.150200.bed.split19802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19803 0 1 2 100 hg38.150200.bed.split19803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19804 0 1 2 100 hg38.150200.bed.split19804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19805 0 1 2 100 hg38.150200.bed.split19805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19806 0 1 2 100 hg38.150200.bed.split19806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19807 0 1 2 100 hg38.150200.bed.split19807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19808 0 1 2 100 hg38.150200.bed.split19808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19809 0 1 2 100 hg38.150200.bed.split19809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1981 0 1 2 100 hg38.150200.bed.split1981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19810 0 1 2 100 hg38.150200.bed.split19810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19811 0 1 2 100 hg38.150200.bed.split19811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19812 0 1 2 100 hg38.150200.bed.split19812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19813 0 1 2 100 hg38.150200.bed.split19813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19814 0 1 2 100 hg38.150200.bed.split19814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19815 0 1 2 100 hg38.150200.bed.split19815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19816 0 1 2 100 hg38.150200.bed.split19816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19817 0 1 2 100 hg38.150200.bed.split19817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19818 0 1 2 100 hg38.150200.bed.split19818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19819 0 1 2 100 hg38.150200.bed.split19819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1982 0 1 2 100 hg38.150200.bed.split1982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19820 0 1 2 100 hg38.150200.bed.split19820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19821 0 1 2 100 hg38.150200.bed.split19821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19822 0 1 2 100 hg38.150200.bed.split19822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19823 0 1 2 100 hg38.150200.bed.split19823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19824 0 1 2 100 hg38.150200.bed.split19824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19825 0 1 2 100 hg38.150200.bed.split19825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19826 0 1 2 100 hg38.150200.bed.split19826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19827 0 1 2 100 hg38.150200.bed.split19827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19828 0 1 2 100 hg38.150200.bed.split19828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19829 0 1 2 100 hg38.150200.bed.split19829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1983 0 1 2 100 hg38.150200.bed.split1983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19830 0 1 2 100 hg38.150200.bed.split19830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19831 0 1 2 100 hg38.150200.bed.split19831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19832 0 1 2 100 hg38.150200.bed.split19832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19833 0 1 2 100 hg38.150200.bed.split19833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19834 0 1 2 100 hg38.150200.bed.split19834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19835 0 1 2 100 hg38.150200.bed.split19835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19836 0 1 2 100 hg38.150200.bed.split19836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19837 0 1 2 100 hg38.150200.bed.split19837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19838 0 1 2 100 hg38.150200.bed.split19838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19839 0 1 2 100 hg38.150200.bed.split19839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1984 0 1 2 100 hg38.150200.bed.split1984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19840 0 1 2 100 hg38.150200.bed.split19840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19841 0 1 2 100 hg38.150200.bed.split19841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19842 0 1 2 100 hg38.150200.bed.split19842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19843 0 1 2 100 hg38.150200.bed.split19843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19844 0 1 2 100 hg38.150200.bed.split19844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19845 0 1 2 100 hg38.150200.bed.split19845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19846 0 1 2 100 hg38.150200.bed.split19846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19847 0 1 2 100 hg38.150200.bed.split19847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19848 0 1 2 100 hg38.150200.bed.split19848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19849 0 1 2 100 hg38.150200.bed.split19849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1985 0 1 2 100 hg38.150200.bed.split1985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19850 0 1 2 100 hg38.150200.bed.split19850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19851 0 1 2 100 hg38.150200.bed.split19851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19852 0 1 2 100 hg38.150200.bed.split19852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19853 0 1 2 100 hg38.150200.bed.split19853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19854 0 1 2 100 hg38.150200.bed.split19854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19855 0 1 2 100 hg38.150200.bed.split19855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19856 0 1 2 100 hg38.150200.bed.split19856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19857 0 1 2 100 hg38.150200.bed.split19857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19858 0 1 2 100 hg38.150200.bed.split19858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19859 0 1 2 100 hg38.150200.bed.split19859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1986 0 1 2 100 hg38.150200.bed.split1986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19860 0 1 2 100 hg38.150200.bed.split19860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19861 0 1 2 100 hg38.150200.bed.split19861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19862 0 1 2 100 hg38.150200.bed.split19862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19863 0 1 2 100 hg38.150200.bed.split19863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19864 0 1 2 100 hg38.150200.bed.split19864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19865 0 1 2 100 hg38.150200.bed.split19865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19866 0 1 2 100 hg38.150200.bed.split19866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19867 0 1 2 100 hg38.150200.bed.split19867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19868 0 1 2 100 hg38.150200.bed.split19868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19869 0 1 2 100 hg38.150200.bed.split19869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1987 0 1 2 100 hg38.150200.bed.split1987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19870 0 1 2 100 hg38.150200.bed.split19870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19871 0 1 2 100 hg38.150200.bed.split19871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19872 0 1 2 100 hg38.150200.bed.split19872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19873 0 1 2 100 hg38.150200.bed.split19873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19874 0 1 2 100 hg38.150200.bed.split19874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19875 0 1 2 100 hg38.150200.bed.split19875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19876 0 1 2 100 hg38.150200.bed.split19876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19877 0 1 2 100 hg38.150200.bed.split19877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19878 0 1 2 100 hg38.150200.bed.split19878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19879 0 1 2 100 hg38.150200.bed.split19879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1988 0 1 2 100 hg38.150200.bed.split1988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19880 0 1 2 100 hg38.150200.bed.split19880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19881 0 1 2 100 hg38.150200.bed.split19881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19882 0 1 2 100 hg38.150200.bed.split19882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19883 0 1 2 100 hg38.150200.bed.split19883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19884 0 1 2 100 hg38.150200.bed.split19884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19885 0 1 2 100 hg38.150200.bed.split19885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19886 0 1 2 100 hg38.150200.bed.split19886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19887 0 1 2 100 hg38.150200.bed.split19887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19888 0 1 2 100 hg38.150200.bed.split19888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19889 0 1 2 100 hg38.150200.bed.split19889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1989 0 1 2 100 hg38.150200.bed.split1989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19890 0 1 2 100 hg38.150200.bed.split19890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19891 0 1 2 100 hg38.150200.bed.split19891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19892 0 1 2 100 hg38.150200.bed.split19892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19893 0 1 2 100 hg38.150200.bed.split19893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19894 0 1 2 100 hg38.150200.bed.split19894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19895 0 1 2 100 hg38.150200.bed.split19895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19896 0 1 2 100 hg38.150200.bed.split19896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19897 0 1 2 100 hg38.150200.bed.split19897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19898 0 1 2 100 hg38.150200.bed.split19898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19899 0 1 2 100 hg38.150200.bed.split19899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split199 0 1 2 100 hg38.150200.bed.split199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1990 0 1 2 100 hg38.150200.bed.split1990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19900 0 1 2 100 hg38.150200.bed.split19900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19901 0 1 2 100 hg38.150200.bed.split19901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19902 0 1 2 100 hg38.150200.bed.split19902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19903 0 1 2 100 hg38.150200.bed.split19903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19904 0 1 2 100 hg38.150200.bed.split19904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19905 0 1 2 100 hg38.150200.bed.split19905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19906 0 1 2 100 hg38.150200.bed.split19906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19907 0 1 2 100 hg38.150200.bed.split19907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19908 0 1 2 100 hg38.150200.bed.split19908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19909 0 1 2 100 hg38.150200.bed.split19909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1991 0 1 2 100 hg38.150200.bed.split1991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19910 0 1 2 100 hg38.150200.bed.split19910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19911 0 1 2 100 hg38.150200.bed.split19911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19912 0 1 2 100 hg38.150200.bed.split19912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19913 0 1 2 100 hg38.150200.bed.split19913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19914 0 1 2 100 hg38.150200.bed.split19914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19915 0 1 2 100 hg38.150200.bed.split19915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19916 0 1 2 100 hg38.150200.bed.split19916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19917 0 1 2 100 hg38.150200.bed.split19917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19918 0 1 2 100 hg38.150200.bed.split19918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19919 0 1 2 100 hg38.150200.bed.split19919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1992 0 1 2 100 hg38.150200.bed.split1992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19920 0 1 2 100 hg38.150200.bed.split19920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19921 0 1 2 100 hg38.150200.bed.split19921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19922 0 1 2 100 hg38.150200.bed.split19922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19923 0 1 2 100 hg38.150200.bed.split19923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19924 0 1 2 100 hg38.150200.bed.split19924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19925 0 1 2 100 hg38.150200.bed.split19925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19926 0 1 2 100 hg38.150200.bed.split19926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19927 0 1 2 100 hg38.150200.bed.split19927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19928 0 1 2 100 hg38.150200.bed.split19928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19929 0 1 2 100 hg38.150200.bed.split19929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1993 0 1 2 100 hg38.150200.bed.split1993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19930 0 1 2 100 hg38.150200.bed.split19930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19931 0 1 2 100 hg38.150200.bed.split19931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19932 0 1 2 100 hg38.150200.bed.split19932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19933 0 1 2 100 hg38.150200.bed.split19933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19934 0 1 2 100 hg38.150200.bed.split19934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19935 0 1 2 100 hg38.150200.bed.split19935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19936 0 1 2 100 hg38.150200.bed.split19936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19937 0 1 2 100 hg38.150200.bed.split19937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19938 0 1 2 100 hg38.150200.bed.split19938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19939 0 1 2 100 hg38.150200.bed.split19939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1994 0 1 2 100 hg38.150200.bed.split1994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19940 0 1 2 100 hg38.150200.bed.split19940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19941 0 1 2 100 hg38.150200.bed.split19941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19942 0 1 2 100 hg38.150200.bed.split19942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19943 0 1 2 100 hg38.150200.bed.split19943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19944 0 1 2 100 hg38.150200.bed.split19944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19945 0 1 2 100 hg38.150200.bed.split19945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19946 0 1 2 100 hg38.150200.bed.split19946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19947 0 1 2 100 hg38.150200.bed.split19947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19948 0 1 2 100 hg38.150200.bed.split19948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19949 0 1 2 100 hg38.150200.bed.split19949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1995 0 1 2 100 hg38.150200.bed.split1995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19950 0 1 2 100 hg38.150200.bed.split19950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19951 0 1 2 100 hg38.150200.bed.split19951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19952 0 1 2 100 hg38.150200.bed.split19952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19953 0 1 2 100 hg38.150200.bed.split19953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19954 0 1 2 100 hg38.150200.bed.split19954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19955 0 1 2 100 hg38.150200.bed.split19955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19956 0 1 2 100 hg38.150200.bed.split19956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19957 0 1 2 100 hg38.150200.bed.split19957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19958 0 1 2 100 hg38.150200.bed.split19958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19959 0 1 2 100 hg38.150200.bed.split19959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1996 0 1 2 100 hg38.150200.bed.split1996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19960 0 1 2 100 hg38.150200.bed.split19960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19961 0 1 2 100 hg38.150200.bed.split19961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19962 0 1 2 100 hg38.150200.bed.split19962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19963 0 1 2 100 hg38.150200.bed.split19963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19964 0 1 2 100 hg38.150200.bed.split19964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19965 0 1 2 100 hg38.150200.bed.split19965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19966 0 1 2 100 hg38.150200.bed.split19966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19967 0 1 2 100 hg38.150200.bed.split19967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19968 0 1 2 100 hg38.150200.bed.split19968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19969 0 1 2 100 hg38.150200.bed.split19969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1997 0 1 2 100 hg38.150200.bed.split1997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19970 0 1 2 100 hg38.150200.bed.split19970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19971 0 1 2 100 hg38.150200.bed.split19971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19972 0 1 2 100 hg38.150200.bed.split19972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19973 0 1 2 100 hg38.150200.bed.split19973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19974 0 1 2 100 hg38.150200.bed.split19974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19975 0 1 2 100 hg38.150200.bed.split19975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19976 0 1 2 100 hg38.150200.bed.split19976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19977 0 1 2 100 hg38.150200.bed.split19977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19978 0 1 2 100 hg38.150200.bed.split19978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19979 0 1 2 100 hg38.150200.bed.split19979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1998 0 1 2 100 hg38.150200.bed.split1998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19980 0 1 2 100 hg38.150200.bed.split19980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19981 0 1 2 100 hg38.150200.bed.split19981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19982 0 1 2 100 hg38.150200.bed.split19982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19983 0 1 2 100 hg38.150200.bed.split19983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19984 0 1 2 100 hg38.150200.bed.split19984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19985 0 1 2 100 hg38.150200.bed.split19985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19986 0 1 2 100 hg38.150200.bed.split19986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19987 0 1 2 100 hg38.150200.bed.split19987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19988 0 1 2 100 hg38.150200.bed.split19988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19989 0 1 2 100 hg38.150200.bed.split19989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split1999 0 1 2 100 hg38.150200.bed.split1999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19990 0 1 2 100 hg38.150200.bed.split19990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19991 0 1 2 100 hg38.150200.bed.split19991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19992 0 1 2 100 hg38.150200.bed.split19992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19993 0 1 2 100 hg38.150200.bed.split19993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19994 0 1 2 100 hg38.150200.bed.split19994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19995 0 1 2 100 hg38.150200.bed.split19995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19996 0 1 2 100 hg38.150200.bed.split19996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19997 0 1 2 100 hg38.150200.bed.split19997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19998 0 1 2 100 hg38.150200.bed.split19998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split19999 0 1 2 100 hg38.150200.bed.split19999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2 0 1 2 100 hg38.150200.bed.split2.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20 0 1 2 100 hg38.150200.bed.split20.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split200 0 1 2 100 hg38.150200.bed.split200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2000 0 1 2 100 hg38.150200.bed.split2000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20000 0 1 2 100 hg38.150200.bed.split20000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20001 0 1 2 100 hg38.150200.bed.split20001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20002 0 1 2 100 hg38.150200.bed.split20002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20003 0 1 2 100 hg38.150200.bed.split20003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20004 0 1 2 100 hg38.150200.bed.split20004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20005 0 1 2 100 hg38.150200.bed.split20005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20006 0 1 2 100 hg38.150200.bed.split20006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20007 0 1 2 100 hg38.150200.bed.split20007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20008 0 1 2 100 hg38.150200.bed.split20008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20009 0 1 2 100 hg38.150200.bed.split20009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2001 0 1 2 100 hg38.150200.bed.split2001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20010 0 1 2 100 hg38.150200.bed.split20010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20011 0 1 2 100 hg38.150200.bed.split20011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20012 0 1 2 100 hg38.150200.bed.split20012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20013 0 1 2 100 hg38.150200.bed.split20013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20014 0 1 2 100 hg38.150200.bed.split20014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20015 0 1 2 100 hg38.150200.bed.split20015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20016 0 1 2 100 hg38.150200.bed.split20016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20017 0 1 2 100 hg38.150200.bed.split20017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20018 0 1 2 100 hg38.150200.bed.split20018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20019 0 1 2 100 hg38.150200.bed.split20019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2002 0 1 2 100 hg38.150200.bed.split2002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20020 0 1 2 100 hg38.150200.bed.split20020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20021 0 1 2 100 hg38.150200.bed.split20021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20022 0 1 2 100 hg38.150200.bed.split20022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20023 0 1 2 100 hg38.150200.bed.split20023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20024 0 1 2 100 hg38.150200.bed.split20024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20025 0 1 2 100 hg38.150200.bed.split20025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20026 0 1 2 100 hg38.150200.bed.split20026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20027 0 1 2 100 hg38.150200.bed.split20027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20028 0 1 2 100 hg38.150200.bed.split20028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20029 0 1 2 100 hg38.150200.bed.split20029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2003 0 1 2 100 hg38.150200.bed.split2003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20030 0 1 2 100 hg38.150200.bed.split20030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20031 0 1 2 100 hg38.150200.bed.split20031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20032 0 1 2 100 hg38.150200.bed.split20032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20033 0 1 2 100 hg38.150200.bed.split20033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20034 0 1 2 100 hg38.150200.bed.split20034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20035 0 1 2 100 hg38.150200.bed.split20035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20036 0 1 2 100 hg38.150200.bed.split20036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20037 0 1 2 100 hg38.150200.bed.split20037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20038 0 1 2 100 hg38.150200.bed.split20038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20039 0 1 2 100 hg38.150200.bed.split20039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2004 0 1 2 100 hg38.150200.bed.split2004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20040 0 1 2 100 hg38.150200.bed.split20040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20041 0 1 2 100 hg38.150200.bed.split20041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20042 0 1 2 100 hg38.150200.bed.split20042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20043 0 1 2 100 hg38.150200.bed.split20043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20044 0 1 2 100 hg38.150200.bed.split20044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20045 0 1 2 100 hg38.150200.bed.split20045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20046 0 1 2 100 hg38.150200.bed.split20046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20047 0 1 2 100 hg38.150200.bed.split20047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20048 0 1 2 100 hg38.150200.bed.split20048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20049 0 1 2 100 hg38.150200.bed.split20049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2005 0 1 2 100 hg38.150200.bed.split2005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20050 0 1 2 100 hg38.150200.bed.split20050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20051 0 1 2 100 hg38.150200.bed.split20051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20052 0 1 2 100 hg38.150200.bed.split20052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20053 0 1 2 100 hg38.150200.bed.split20053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20054 0 1 2 100 hg38.150200.bed.split20054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20055 0 1 2 100 hg38.150200.bed.split20055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20056 0 1 2 100 hg38.150200.bed.split20056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20057 0 1 2 100 hg38.150200.bed.split20057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20058 0 1 2 100 hg38.150200.bed.split20058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20059 0 1 2 100 hg38.150200.bed.split20059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2006 0 1 2 100 hg38.150200.bed.split2006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20060 0 1 2 100 hg38.150200.bed.split20060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20061 0 1 2 100 hg38.150200.bed.split20061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20062 0 1 2 100 hg38.150200.bed.split20062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20063 0 1 2 100 hg38.150200.bed.split20063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20064 0 1 2 100 hg38.150200.bed.split20064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20065 0 1 2 100 hg38.150200.bed.split20065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20066 0 1 2 100 hg38.150200.bed.split20066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20067 0 1 2 100 hg38.150200.bed.split20067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20068 0 1 2 100 hg38.150200.bed.split20068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20069 0 1 2 100 hg38.150200.bed.split20069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2007 0 1 2 100 hg38.150200.bed.split2007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20070 0 1 2 100 hg38.150200.bed.split20070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20071 0 1 2 100 hg38.150200.bed.split20071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20072 0 1 2 100 hg38.150200.bed.split20072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20073 0 1 2 100 hg38.150200.bed.split20073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20074 0 1 2 100 hg38.150200.bed.split20074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20075 0 1 2 100 hg38.150200.bed.split20075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20076 0 1 2 100 hg38.150200.bed.split20076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20077 0 1 2 100 hg38.150200.bed.split20077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20078 0 1 2 100 hg38.150200.bed.split20078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20079 0 1 2 100 hg38.150200.bed.split20079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2008 0 1 2 100 hg38.150200.bed.split2008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20080 0 1 2 100 hg38.150200.bed.split20080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20081 0 1 2 100 hg38.150200.bed.split20081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20082 0 1 2 100 hg38.150200.bed.split20082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20083 0 1 2 100 hg38.150200.bed.split20083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20084 0 1 2 100 hg38.150200.bed.split20084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20085 0 1 2 100 hg38.150200.bed.split20085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20086 0 1 2 100 hg38.150200.bed.split20086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20087 0 1 2 100 hg38.150200.bed.split20087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20088 0 1 2 100 hg38.150200.bed.split20088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20089 0 1 2 100 hg38.150200.bed.split20089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2009 0 1 2 100 hg38.150200.bed.split2009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20090 0 1 2 100 hg38.150200.bed.split20090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20091 0 1 2 100 hg38.150200.bed.split20091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20092 0 1 2 100 hg38.150200.bed.split20092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20093 0 1 2 100 hg38.150200.bed.split20093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20094 0 1 2 100 hg38.150200.bed.split20094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20095 0 1 2 100 hg38.150200.bed.split20095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20096 0 1 2 100 hg38.150200.bed.split20096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20097 0 1 2 100 hg38.150200.bed.split20097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20098 0 1 2 100 hg38.150200.bed.split20098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20099 0 1 2 100 hg38.150200.bed.split20099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split201 0 1 2 100 hg38.150200.bed.split201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2010 0 1 2 100 hg38.150200.bed.split2010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20100 0 1 2 100 hg38.150200.bed.split20100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20101 0 1 2 100 hg38.150200.bed.split20101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20102 0 1 2 100 hg38.150200.bed.split20102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20103 0 1 2 100 hg38.150200.bed.split20103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20104 0 1 2 100 hg38.150200.bed.split20104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20105 0 1 2 100 hg38.150200.bed.split20105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20106 0 1 2 100 hg38.150200.bed.split20106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20107 0 1 2 100 hg38.150200.bed.split20107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20108 0 1 2 100 hg38.150200.bed.split20108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20109 0 1 2 100 hg38.150200.bed.split20109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2011 0 1 2 100 hg38.150200.bed.split2011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20110 0 1 2 100 hg38.150200.bed.split20110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20111 0 1 2 100 hg38.150200.bed.split20111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20112 0 1 2 100 hg38.150200.bed.split20112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20113 0 1 2 100 hg38.150200.bed.split20113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20114 0 1 2 100 hg38.150200.bed.split20114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20115 0 1 2 100 hg38.150200.bed.split20115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20116 0 1 2 100 hg38.150200.bed.split20116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20117 0 1 2 100 hg38.150200.bed.split20117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20118 0 1 2 100 hg38.150200.bed.split20118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20119 0 1 2 100 hg38.150200.bed.split20119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2012 0 1 2 100 hg38.150200.bed.split2012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20120 0 1 2 100 hg38.150200.bed.split20120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20121 0 1 2 100 hg38.150200.bed.split20121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20122 0 1 2 100 hg38.150200.bed.split20122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20123 0 1 2 100 hg38.150200.bed.split20123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20124 0 1 2 100 hg38.150200.bed.split20124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20125 0 1 2 100 hg38.150200.bed.split20125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20126 0 1 2 100 hg38.150200.bed.split20126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20127 0 1 2 100 hg38.150200.bed.split20127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20128 0 1 2 100 hg38.150200.bed.split20128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20129 0 1 2 100 hg38.150200.bed.split20129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2013 0 1 2 100 hg38.150200.bed.split2013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20130 0 1 2 100 hg38.150200.bed.split20130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20131 0 1 2 100 hg38.150200.bed.split20131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20132 0 1 2 100 hg38.150200.bed.split20132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20133 0 1 2 100 hg38.150200.bed.split20133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20134 0 1 2 100 hg38.150200.bed.split20134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20135 0 1 2 100 hg38.150200.bed.split20135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20136 0 1 2 100 hg38.150200.bed.split20136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20137 0 1 2 100 hg38.150200.bed.split20137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20138 0 1 2 100 hg38.150200.bed.split20138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20139 0 1 2 100 hg38.150200.bed.split20139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2014 0 1 2 100 hg38.150200.bed.split2014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20140 0 1 2 100 hg38.150200.bed.split20140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20141 0 1 2 100 hg38.150200.bed.split20141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20142 0 1 2 100 hg38.150200.bed.split20142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20143 0 1 2 100 hg38.150200.bed.split20143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20144 0 1 2 100 hg38.150200.bed.split20144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20145 0 1 2 100 hg38.150200.bed.split20145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20146 0 1 2 100 hg38.150200.bed.split20146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20147 0 1 2 100 hg38.150200.bed.split20147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20148 0 1 2 100 hg38.150200.bed.split20148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20149 0 1 2 100 hg38.150200.bed.split20149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2015 0 1 2 100 hg38.150200.bed.split2015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20150 0 1 2 100 hg38.150200.bed.split20150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20151 0 1 2 100 hg38.150200.bed.split20151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20152 0 1 2 100 hg38.150200.bed.split20152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20153 0 1 2 100 hg38.150200.bed.split20153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20154 0 1 2 100 hg38.150200.bed.split20154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20155 0 1 2 100 hg38.150200.bed.split20155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20156 0 1 2 100 hg38.150200.bed.split20156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20157 0 1 2 100 hg38.150200.bed.split20157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20158 0 1 2 100 hg38.150200.bed.split20158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20159 0 1 2 100 hg38.150200.bed.split20159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2016 0 1 2 100 hg38.150200.bed.split2016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20160 0 1 2 100 hg38.150200.bed.split20160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20161 0 1 2 100 hg38.150200.bed.split20161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20162 0 1 2 100 hg38.150200.bed.split20162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20163 0 1 2 100 hg38.150200.bed.split20163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20164 0 1 2 100 hg38.150200.bed.split20164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20165 0 1 2 100 hg38.150200.bed.split20165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20166 0 1 2 100 hg38.150200.bed.split20166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20167 0 1 2 100 hg38.150200.bed.split20167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20168 0 1 2 100 hg38.150200.bed.split20168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20169 0 1 2 100 hg38.150200.bed.split20169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2017 0 1 2 100 hg38.150200.bed.split2017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20170 0 1 2 100 hg38.150200.bed.split20170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20171 0 1 2 100 hg38.150200.bed.split20171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20172 0 1 2 100 hg38.150200.bed.split20172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20173 0 1 2 100 hg38.150200.bed.split20173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20174 0 1 2 100 hg38.150200.bed.split20174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20175 0 1 2 100 hg38.150200.bed.split20175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20176 0 1 2 100 hg38.150200.bed.split20176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20177 0 1 2 100 hg38.150200.bed.split20177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20178 0 1 2 100 hg38.150200.bed.split20178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20179 0 1 2 100 hg38.150200.bed.split20179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2018 0 1 2 100 hg38.150200.bed.split2018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20180 0 1 2 100 hg38.150200.bed.split20180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20181 0 1 2 100 hg38.150200.bed.split20181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20182 0 1 2 100 hg38.150200.bed.split20182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20183 0 1 2 100 hg38.150200.bed.split20183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20184 0 1 2 100 hg38.150200.bed.split20184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20185 0 1 2 100 hg38.150200.bed.split20185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20186 0 1 2 100 hg38.150200.bed.split20186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20187 0 1 2 100 hg38.150200.bed.split20187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20188 0 1 2 100 hg38.150200.bed.split20188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20189 0 1 2 100 hg38.150200.bed.split20189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2019 0 1 2 100 hg38.150200.bed.split2019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20190 0 1 2 100 hg38.150200.bed.split20190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20191 0 1 2 100 hg38.150200.bed.split20191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20192 0 1 2 100 hg38.150200.bed.split20192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20193 0 1 2 100 hg38.150200.bed.split20193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20194 0 1 2 100 hg38.150200.bed.split20194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20195 0 1 2 100 hg38.150200.bed.split20195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20196 0 1 2 100 hg38.150200.bed.split20196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20197 0 1 2 100 hg38.150200.bed.split20197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20198 0 1 2 100 hg38.150200.bed.split20198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20199 0 1 2 100 hg38.150200.bed.split20199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split202 0 1 2 100 hg38.150200.bed.split202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2020 0 1 2 100 hg38.150200.bed.split2020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20200 0 1 2 100 hg38.150200.bed.split20200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20201 0 1 2 100 hg38.150200.bed.split20201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20202 0 1 2 100 hg38.150200.bed.split20202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20203 0 1 2 100 hg38.150200.bed.split20203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20204 0 1 2 100 hg38.150200.bed.split20204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20205 0 1 2 100 hg38.150200.bed.split20205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20206 0 1 2 100 hg38.150200.bed.split20206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20207 0 1 2 100 hg38.150200.bed.split20207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20208 0 1 2 100 hg38.150200.bed.split20208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20209 0 1 2 100 hg38.150200.bed.split20209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2021 0 1 2 100 hg38.150200.bed.split2021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20210 0 1 2 100 hg38.150200.bed.split20210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20211 0 1 2 100 hg38.150200.bed.split20211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20212 0 1 2 100 hg38.150200.bed.split20212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20213 0 1 2 100 hg38.150200.bed.split20213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20214 0 1 2 100 hg38.150200.bed.split20214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20215 0 1 2 100 hg38.150200.bed.split20215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20216 0 1 2 100 hg38.150200.bed.split20216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20217 0 1 2 100 hg38.150200.bed.split20217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20218 0 1 2 100 hg38.150200.bed.split20218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20219 0 1 2 100 hg38.150200.bed.split20219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2022 0 1 2 100 hg38.150200.bed.split2022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20220 0 1 2 100 hg38.150200.bed.split20220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20221 0 1 2 100 hg38.150200.bed.split20221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20222 0 1 2 100 hg38.150200.bed.split20222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20223 0 1 2 100 hg38.150200.bed.split20223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20224 0 1 2 100 hg38.150200.bed.split20224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20225 0 1 2 100 hg38.150200.bed.split20225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20226 0 1 2 100 hg38.150200.bed.split20226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20227 0 1 2 100 hg38.150200.bed.split20227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20228 0 1 2 100 hg38.150200.bed.split20228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20229 0 1 2 100 hg38.150200.bed.split20229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2023 0 1 2 100 hg38.150200.bed.split2023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20230 0 1 2 100 hg38.150200.bed.split20230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20231 0 1 2 100 hg38.150200.bed.split20231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20232 0 1 2 100 hg38.150200.bed.split20232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20233 0 1 2 100 hg38.150200.bed.split20233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20234 0 1 2 100 hg38.150200.bed.split20234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20235 0 1 2 100 hg38.150200.bed.split20235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20236 0 1 2 100 hg38.150200.bed.split20236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20237 0 1 2 100 hg38.150200.bed.split20237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20238 0 1 2 100 hg38.150200.bed.split20238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20239 0 1 2 100 hg38.150200.bed.split20239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2024 0 1 2 100 hg38.150200.bed.split2024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20240 0 1 2 100 hg38.150200.bed.split20240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20241 0 1 2 100 hg38.150200.bed.split20241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20242 0 1 2 100 hg38.150200.bed.split20242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20243 0 1 2 100 hg38.150200.bed.split20243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20244 0 1 2 100 hg38.150200.bed.split20244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20245 0 1 2 100 hg38.150200.bed.split20245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20246 0 1 2 100 hg38.150200.bed.split20246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20247 0 1 2 100 hg38.150200.bed.split20247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20248 0 1 2 100 hg38.150200.bed.split20248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20249 0 1 2 100 hg38.150200.bed.split20249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2025 0 1 2 100 hg38.150200.bed.split2025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20250 0 1 2 100 hg38.150200.bed.split20250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20251 0 1 2 100 hg38.150200.bed.split20251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20252 0 1 2 100 hg38.150200.bed.split20252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20253 0 1 2 100 hg38.150200.bed.split20253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20254 0 1 2 100 hg38.150200.bed.split20254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20255 0 1 2 100 hg38.150200.bed.split20255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20256 0 1 2 100 hg38.150200.bed.split20256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20257 0 1 2 100 hg38.150200.bed.split20257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20258 0 1 2 100 hg38.150200.bed.split20258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20259 0 1 2 100 hg38.150200.bed.split20259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2026 0 1 2 100 hg38.150200.bed.split2026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20260 0 1 2 100 hg38.150200.bed.split20260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20261 0 1 2 100 hg38.150200.bed.split20261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20262 0 1 2 100 hg38.150200.bed.split20262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20263 0 1 2 100 hg38.150200.bed.split20263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20264 0 1 2 100 hg38.150200.bed.split20264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20265 0 1 2 100 hg38.150200.bed.split20265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20266 0 1 2 100 hg38.150200.bed.split20266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20267 0 1 2 100 hg38.150200.bed.split20267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20268 0 1 2 100 hg38.150200.bed.split20268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20269 0 1 2 100 hg38.150200.bed.split20269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2027 0 1 2 100 hg38.150200.bed.split2027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20270 0 1 2 100 hg38.150200.bed.split20270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20271 0 1 2 100 hg38.150200.bed.split20271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20272 0 1 2 100 hg38.150200.bed.split20272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20273 0 1 2 100 hg38.150200.bed.split20273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20274 0 1 2 100 hg38.150200.bed.split20274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20275 0 1 2 100 hg38.150200.bed.split20275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20276 0 1 2 100 hg38.150200.bed.split20276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20277 0 1 2 100 hg38.150200.bed.split20277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20278 0 1 2 100 hg38.150200.bed.split20278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20279 0 1 2 100 hg38.150200.bed.split20279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2028 0 1 2 100 hg38.150200.bed.split2028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20280 0 1 2 100 hg38.150200.bed.split20280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20281 0 1 2 100 hg38.150200.bed.split20281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20282 0 1 2 100 hg38.150200.bed.split20282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20283 0 1 2 100 hg38.150200.bed.split20283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20284 0 1 2 100 hg38.150200.bed.split20284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20285 0 1 2 100 hg38.150200.bed.split20285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20286 0 1 2 100 hg38.150200.bed.split20286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20287 0 1 2 100 hg38.150200.bed.split20287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20288 0 1 2 100 hg38.150200.bed.split20288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20289 0 1 2 100 hg38.150200.bed.split20289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2029 0 1 2 100 hg38.150200.bed.split2029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20290 0 1 2 100 hg38.150200.bed.split20290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20291 0 1 2 100 hg38.150200.bed.split20291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20292 0 1 2 100 hg38.150200.bed.split20292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20293 0 1 2 100 hg38.150200.bed.split20293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20294 0 1 2 100 hg38.150200.bed.split20294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20295 0 1 2 100 hg38.150200.bed.split20295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20296 0 1 2 100 hg38.150200.bed.split20296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20297 0 1 2 100 hg38.150200.bed.split20297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20298 0 1 2 100 hg38.150200.bed.split20298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20299 0 1 2 100 hg38.150200.bed.split20299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split203 0 1 2 100 hg38.150200.bed.split203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2030 0 1 2 100 hg38.150200.bed.split2030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20300 0 1 2 100 hg38.150200.bed.split20300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20301 0 1 2 100 hg38.150200.bed.split20301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20302 0 1 2 100 hg38.150200.bed.split20302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20303 0 1 2 100 hg38.150200.bed.split20303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20304 0 1 2 100 hg38.150200.bed.split20304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20305 0 1 2 100 hg38.150200.bed.split20305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20306 0 1 2 100 hg38.150200.bed.split20306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20307 0 1 2 100 hg38.150200.bed.split20307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20308 0 1 2 100 hg38.150200.bed.split20308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20309 0 1 2 100 hg38.150200.bed.split20309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2031 0 1 2 100 hg38.150200.bed.split2031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20310 0 1 2 100 hg38.150200.bed.split20310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20311 0 1 2 100 hg38.150200.bed.split20311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20312 0 1 2 100 hg38.150200.bed.split20312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20313 0 1 2 100 hg38.150200.bed.split20313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20314 0 1 2 100 hg38.150200.bed.split20314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20315 0 1 2 100 hg38.150200.bed.split20315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20316 0 1 2 100 hg38.150200.bed.split20316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20317 0 1 2 100 hg38.150200.bed.split20317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20318 0 1 2 100 hg38.150200.bed.split20318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20319 0 1 2 100 hg38.150200.bed.split20319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2032 0 1 2 100 hg38.150200.bed.split2032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20320 0 1 2 100 hg38.150200.bed.split20320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20321 0 1 2 100 hg38.150200.bed.split20321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20322 0 1 2 100 hg38.150200.bed.split20322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20323 0 1 2 100 hg38.150200.bed.split20323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20324 0 1 2 100 hg38.150200.bed.split20324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20325 0 1 2 100 hg38.150200.bed.split20325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20326 0 1 2 100 hg38.150200.bed.split20326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20327 0 1 2 100 hg38.150200.bed.split20327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20328 0 1 2 100 hg38.150200.bed.split20328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20329 0 1 2 100 hg38.150200.bed.split20329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2033 0 1 2 100 hg38.150200.bed.split2033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20330 0 1 2 100 hg38.150200.bed.split20330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20331 0 1 2 100 hg38.150200.bed.split20331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20332 0 1 2 100 hg38.150200.bed.split20332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20333 0 1 2 100 hg38.150200.bed.split20333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20334 0 1 2 100 hg38.150200.bed.split20334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20335 0 1 2 100 hg38.150200.bed.split20335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20336 0 1 2 100 hg38.150200.bed.split20336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20337 0 1 2 100 hg38.150200.bed.split20337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20338 0 1 2 100 hg38.150200.bed.split20338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20339 0 1 2 100 hg38.150200.bed.split20339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2034 0 1 2 100 hg38.150200.bed.split2034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20340 0 1 2 100 hg38.150200.bed.split20340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20341 0 1 2 100 hg38.150200.bed.split20341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20342 0 1 2 100 hg38.150200.bed.split20342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20343 0 1 2 100 hg38.150200.bed.split20343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20344 0 1 2 100 hg38.150200.bed.split20344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20345 0 1 2 100 hg38.150200.bed.split20345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20346 0 1 2 100 hg38.150200.bed.split20346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20347 0 1 2 100 hg38.150200.bed.split20347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20348 0 1 2 100 hg38.150200.bed.split20348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20349 0 1 2 100 hg38.150200.bed.split20349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2035 0 1 2 100 hg38.150200.bed.split2035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20350 0 1 2 100 hg38.150200.bed.split20350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20351 0 1 2 100 hg38.150200.bed.split20351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20352 0 1 2 100 hg38.150200.bed.split20352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20353 0 1 2 100 hg38.150200.bed.split20353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20354 0 1 2 100 hg38.150200.bed.split20354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20355 0 1 2 100 hg38.150200.bed.split20355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20356 0 1 2 100 hg38.150200.bed.split20356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20357 0 1 2 100 hg38.150200.bed.split20357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20358 0 1 2 100 hg38.150200.bed.split20358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20359 0 1 2 100 hg38.150200.bed.split20359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2036 0 1 2 100 hg38.150200.bed.split2036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20360 0 1 2 100 hg38.150200.bed.split20360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20361 0 1 2 100 hg38.150200.bed.split20361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20362 0 1 2 100 hg38.150200.bed.split20362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20363 0 1 2 100 hg38.150200.bed.split20363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20364 0 1 2 100 hg38.150200.bed.split20364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20365 0 1 2 100 hg38.150200.bed.split20365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20366 0 1 2 100 hg38.150200.bed.split20366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20367 0 1 2 100 hg38.150200.bed.split20367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20368 0 1 2 100 hg38.150200.bed.split20368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20369 0 1 2 100 hg38.150200.bed.split20369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2037 0 1 2 100 hg38.150200.bed.split2037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20370 0 1 2 100 hg38.150200.bed.split20370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20371 0 1 2 100 hg38.150200.bed.split20371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20372 0 1 2 100 hg38.150200.bed.split20372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20373 0 1 2 100 hg38.150200.bed.split20373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20374 0 1 2 100 hg38.150200.bed.split20374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20375 0 1 2 100 hg38.150200.bed.split20375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20376 0 1 2 100 hg38.150200.bed.split20376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20377 0 1 2 100 hg38.150200.bed.split20377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20378 0 1 2 100 hg38.150200.bed.split20378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20379 0 1 2 100 hg38.150200.bed.split20379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2038 0 1 2 100 hg38.150200.bed.split2038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20380 0 1 2 100 hg38.150200.bed.split20380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20381 0 1 2 100 hg38.150200.bed.split20381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20382 0 1 2 100 hg38.150200.bed.split20382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20383 0 1 2 100 hg38.150200.bed.split20383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20384 0 1 2 100 hg38.150200.bed.split20384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20385 0 1 2 100 hg38.150200.bed.split20385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20386 0 1 2 100 hg38.150200.bed.split20386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20387 0 1 2 100 hg38.150200.bed.split20387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20388 0 1 2 100 hg38.150200.bed.split20388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20389 0 1 2 100 hg38.150200.bed.split20389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2039 0 1 2 100 hg38.150200.bed.split2039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20390 0 1 2 100 hg38.150200.bed.split20390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20391 0 1 2 100 hg38.150200.bed.split20391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20392 0 1 2 100 hg38.150200.bed.split20392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20393 0 1 2 100 hg38.150200.bed.split20393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20394 0 1 2 100 hg38.150200.bed.split20394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20395 0 1 2 100 hg38.150200.bed.split20395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20396 0 1 2 100 hg38.150200.bed.split20396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20397 0 1 2 100 hg38.150200.bed.split20397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20398 0 1 2 100 hg38.150200.bed.split20398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20399 0 1 2 100 hg38.150200.bed.split20399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split204 0 1 2 100 hg38.150200.bed.split204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2040 0 1 2 100 hg38.150200.bed.split2040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20400 0 1 2 100 hg38.150200.bed.split20400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20401 0 1 2 100 hg38.150200.bed.split20401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20402 0 1 2 100 hg38.150200.bed.split20402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20403 0 1 2 100 hg38.150200.bed.split20403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20404 0 1 2 100 hg38.150200.bed.split20404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20405 0 1 2 100 hg38.150200.bed.split20405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20406 0 1 2 100 hg38.150200.bed.split20406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20407 0 1 2 100 hg38.150200.bed.split20407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20408 0 1 2 100 hg38.150200.bed.split20408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20409 0 1 2 100 hg38.150200.bed.split20409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2041 0 1 2 100 hg38.150200.bed.split2041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20410 0 1 2 100 hg38.150200.bed.split20410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20411 0 1 2 100 hg38.150200.bed.split20411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20412 0 1 2 100 hg38.150200.bed.split20412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20413 0 1 2 100 hg38.150200.bed.split20413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20414 0 1 2 100 hg38.150200.bed.split20414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20415 0 1 2 100 hg38.150200.bed.split20415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20416 0 1 2 100 hg38.150200.bed.split20416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20417 0 1 2 100 hg38.150200.bed.split20417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20418 0 1 2 100 hg38.150200.bed.split20418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20419 0 1 2 100 hg38.150200.bed.split20419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2042 0 1 2 100 hg38.150200.bed.split2042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20420 0 1 2 100 hg38.150200.bed.split20420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20421 0 1 2 100 hg38.150200.bed.split20421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20422 0 1 2 100 hg38.150200.bed.split20422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20423 0 1 2 100 hg38.150200.bed.split20423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20424 0 1 2 100 hg38.150200.bed.split20424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20425 0 1 2 100 hg38.150200.bed.split20425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20426 0 1 2 100 hg38.150200.bed.split20426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20427 0 1 2 100 hg38.150200.bed.split20427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20428 0 1 2 100 hg38.150200.bed.split20428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20429 0 1 2 100 hg38.150200.bed.split20429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2043 0 1 2 100 hg38.150200.bed.split2043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20430 0 1 2 100 hg38.150200.bed.split20430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20431 0 1 2 100 hg38.150200.bed.split20431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20432 0 1 2 100 hg38.150200.bed.split20432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20433 0 1 2 100 hg38.150200.bed.split20433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20434 0 1 2 100 hg38.150200.bed.split20434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20435 0 1 2 100 hg38.150200.bed.split20435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20436 0 1 2 100 hg38.150200.bed.split20436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20437 0 1 2 100 hg38.150200.bed.split20437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20438 0 1 2 100 hg38.150200.bed.split20438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20439 0 1 2 100 hg38.150200.bed.split20439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2044 0 1 2 100 hg38.150200.bed.split2044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20440 0 1 2 100 hg38.150200.bed.split20440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20441 0 1 2 100 hg38.150200.bed.split20441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20442 0 1 2 100 hg38.150200.bed.split20442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20443 0 1 2 100 hg38.150200.bed.split20443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20444 0 1 2 100 hg38.150200.bed.split20444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20445 0 1 2 100 hg38.150200.bed.split20445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20446 0 1 2 100 hg38.150200.bed.split20446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20447 0 1 2 100 hg38.150200.bed.split20447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20448 0 1 2 100 hg38.150200.bed.split20448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20449 0 1 2 100 hg38.150200.bed.split20449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2045 0 1 2 100 hg38.150200.bed.split2045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20450 0 1 2 100 hg38.150200.bed.split20450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20451 0 1 2 100 hg38.150200.bed.split20451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20452 0 1 2 100 hg38.150200.bed.split20452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20453 0 1 2 100 hg38.150200.bed.split20453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20454 0 1 2 100 hg38.150200.bed.split20454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20455 0 1 2 100 hg38.150200.bed.split20455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20456 0 1 2 100 hg38.150200.bed.split20456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20457 0 1 2 100 hg38.150200.bed.split20457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20458 0 1 2 100 hg38.150200.bed.split20458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20459 0 1 2 100 hg38.150200.bed.split20459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2046 0 1 2 100 hg38.150200.bed.split2046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20460 0 1 2 100 hg38.150200.bed.split20460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20461 0 1 2 100 hg38.150200.bed.split20461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20462 0 1 2 100 hg38.150200.bed.split20462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20463 0 1 2 100 hg38.150200.bed.split20463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20464 0 1 2 100 hg38.150200.bed.split20464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20465 0 1 2 100 hg38.150200.bed.split20465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20466 0 1 2 100 hg38.150200.bed.split20466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20467 0 1 2 100 hg38.150200.bed.split20467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20468 0 1 2 100 hg38.150200.bed.split20468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20469 0 1 2 100 hg38.150200.bed.split20469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2047 0 1 2 100 hg38.150200.bed.split2047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20470 0 1 2 100 hg38.150200.bed.split20470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20471 0 1 2 100 hg38.150200.bed.split20471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20472 0 1 2 100 hg38.150200.bed.split20472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20473 0 1 2 100 hg38.150200.bed.split20473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20474 0 1 2 100 hg38.150200.bed.split20474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20475 0 1 2 100 hg38.150200.bed.split20475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20476 0 1 2 100 hg38.150200.bed.split20476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20477 0 1 2 100 hg38.150200.bed.split20477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20478 0 1 2 100 hg38.150200.bed.split20478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20479 0 1 2 100 hg38.150200.bed.split20479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2048 0 1 2 100 hg38.150200.bed.split2048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20480 0 1 2 100 hg38.150200.bed.split20480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20481 0 1 2 100 hg38.150200.bed.split20481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20482 0 1 2 100 hg38.150200.bed.split20482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20483 0 1 2 100 hg38.150200.bed.split20483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20484 0 1 2 100 hg38.150200.bed.split20484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20485 0 1 2 100 hg38.150200.bed.split20485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20486 0 1 2 100 hg38.150200.bed.split20486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20487 0 1 2 100 hg38.150200.bed.split20487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20488 0 1 2 100 hg38.150200.bed.split20488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20489 0 1 2 100 hg38.150200.bed.split20489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2049 0 1 2 100 hg38.150200.bed.split2049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20490 0 1 2 100 hg38.150200.bed.split20490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20491 0 1 2 100 hg38.150200.bed.split20491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20492 0 1 2 100 hg38.150200.bed.split20492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20493 0 1 2 100 hg38.150200.bed.split20493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20494 0 1 2 100 hg38.150200.bed.split20494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20495 0 1 2 100 hg38.150200.bed.split20495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20496 0 1 2 100 hg38.150200.bed.split20496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20497 0 1 2 100 hg38.150200.bed.split20497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20498 0 1 2 100 hg38.150200.bed.split20498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20499 0 1 2 100 hg38.150200.bed.split20499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split205 0 1 2 100 hg38.150200.bed.split205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2050 0 1 2 100 hg38.150200.bed.split2050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20500 0 1 2 100 hg38.150200.bed.split20500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20501 0 1 2 100 hg38.150200.bed.split20501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20502 0 1 2 100 hg38.150200.bed.split20502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20503 0 1 2 100 hg38.150200.bed.split20503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20504 0 1 2 100 hg38.150200.bed.split20504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20505 0 1 2 100 hg38.150200.bed.split20505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20506 0 1 2 100 hg38.150200.bed.split20506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20507 0 1 2 100 hg38.150200.bed.split20507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20508 0 1 2 100 hg38.150200.bed.split20508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20509 0 1 2 100 hg38.150200.bed.split20509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2051 0 1 2 100 hg38.150200.bed.split2051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20510 0 1 2 100 hg38.150200.bed.split20510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20511 0 1 2 100 hg38.150200.bed.split20511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20512 0 1 2 100 hg38.150200.bed.split20512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20513 0 1 2 100 hg38.150200.bed.split20513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20514 0 1 2 100 hg38.150200.bed.split20514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20515 0 1 2 100 hg38.150200.bed.split20515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20516 0 1 2 100 hg38.150200.bed.split20516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20517 0 1 2 100 hg38.150200.bed.split20517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20518 0 1 2 100 hg38.150200.bed.split20518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20519 0 1 2 100 hg38.150200.bed.split20519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2052 0 1 2 100 hg38.150200.bed.split2052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20520 0 1 2 100 hg38.150200.bed.split20520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20521 0 1 2 100 hg38.150200.bed.split20521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20522 0 1 2 100 hg38.150200.bed.split20522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20523 0 1 2 100 hg38.150200.bed.split20523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20524 0 1 2 100 hg38.150200.bed.split20524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20525 0 1 2 100 hg38.150200.bed.split20525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20526 0 1 2 100 hg38.150200.bed.split20526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20527 0 1 2 100 hg38.150200.bed.split20527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20528 0 1 2 100 hg38.150200.bed.split20528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20529 0 1 2 100 hg38.150200.bed.split20529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2053 0 1 2 100 hg38.150200.bed.split2053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20530 0 1 2 100 hg38.150200.bed.split20530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20531 0 1 2 100 hg38.150200.bed.split20531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20532 0 1 2 100 hg38.150200.bed.split20532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20533 0 1 2 100 hg38.150200.bed.split20533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20534 0 1 2 100 hg38.150200.bed.split20534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20535 0 1 2 100 hg38.150200.bed.split20535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20536 0 1 2 100 hg38.150200.bed.split20536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20537 0 1 2 100 hg38.150200.bed.split20537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20538 0 1 2 100 hg38.150200.bed.split20538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20539 0 1 2 100 hg38.150200.bed.split20539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2054 0 1 2 100 hg38.150200.bed.split2054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20540 0 1 2 100 hg38.150200.bed.split20540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20541 0 1 2 100 hg38.150200.bed.split20541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20542 0 1 2 100 hg38.150200.bed.split20542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20543 0 1 2 100 hg38.150200.bed.split20543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20544 0 1 2 100 hg38.150200.bed.split20544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20545 0 1 2 100 hg38.150200.bed.split20545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20546 0 1 2 100 hg38.150200.bed.split20546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20547 0 1 2 100 hg38.150200.bed.split20547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20548 0 1 2 100 hg38.150200.bed.split20548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20549 0 1 2 100 hg38.150200.bed.split20549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2055 0 1 2 100 hg38.150200.bed.split2055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20550 0 1 2 100 hg38.150200.bed.split20550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20551 0 1 2 100 hg38.150200.bed.split20551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20552 0 1 2 100 hg38.150200.bed.split20552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20553 0 1 2 100 hg38.150200.bed.split20553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20554 0 1 2 100 hg38.150200.bed.split20554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20555 0 1 2 100 hg38.150200.bed.split20555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20556 0 1 2 100 hg38.150200.bed.split20556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20557 0 1 2 100 hg38.150200.bed.split20557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20558 0 1 2 100 hg38.150200.bed.split20558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20559 0 1 2 100 hg38.150200.bed.split20559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2056 0 1 2 100 hg38.150200.bed.split2056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20560 0 1 2 100 hg38.150200.bed.split20560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20561 0 1 2 100 hg38.150200.bed.split20561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20562 0 1 2 100 hg38.150200.bed.split20562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20563 0 1 2 100 hg38.150200.bed.split20563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20564 0 1 2 100 hg38.150200.bed.split20564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20565 0 1 2 100 hg38.150200.bed.split20565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20566 0 1 2 100 hg38.150200.bed.split20566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20567 0 1 2 100 hg38.150200.bed.split20567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20568 0 1 2 100 hg38.150200.bed.split20568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20569 0 1 2 100 hg38.150200.bed.split20569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2057 0 1 2 100 hg38.150200.bed.split2057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20570 0 1 2 100 hg38.150200.bed.split20570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20571 0 1 2 100 hg38.150200.bed.split20571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20572 0 1 2 100 hg38.150200.bed.split20572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20573 0 1 2 100 hg38.150200.bed.split20573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20574 0 1 2 100 hg38.150200.bed.split20574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20575 0 1 2 100 hg38.150200.bed.split20575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20576 0 1 2 100 hg38.150200.bed.split20576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20577 0 1 2 100 hg38.150200.bed.split20577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20578 0 1 2 100 hg38.150200.bed.split20578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20579 0 1 2 100 hg38.150200.bed.split20579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2058 0 1 2 100 hg38.150200.bed.split2058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20580 0 1 2 100 hg38.150200.bed.split20580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20581 0 1 2 100 hg38.150200.bed.split20581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20582 0 1 2 100 hg38.150200.bed.split20582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20583 0 1 2 100 hg38.150200.bed.split20583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20584 0 1 2 100 hg38.150200.bed.split20584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20585 0 1 2 100 hg38.150200.bed.split20585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20586 0 1 2 100 hg38.150200.bed.split20586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20587 0 1 2 100 hg38.150200.bed.split20587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20588 0 1 2 100 hg38.150200.bed.split20588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20589 0 1 2 100 hg38.150200.bed.split20589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2059 0 1 2 100 hg38.150200.bed.split2059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20590 0 1 2 100 hg38.150200.bed.split20590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20591 0 1 2 100 hg38.150200.bed.split20591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20592 0 1 2 100 hg38.150200.bed.split20592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20593 0 1 2 100 hg38.150200.bed.split20593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20594 0 1 2 100 hg38.150200.bed.split20594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20595 0 1 2 100 hg38.150200.bed.split20595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20596 0 1 2 100 hg38.150200.bed.split20596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20597 0 1 2 100 hg38.150200.bed.split20597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20598 0 1 2 100 hg38.150200.bed.split20598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20599 0 1 2 100 hg38.150200.bed.split20599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split206 0 1 2 100 hg38.150200.bed.split206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2060 0 1 2 100 hg38.150200.bed.split2060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split20600 0 1 2 100 hg38.150200.bed.split20600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2061 0 1 2 100 hg38.150200.bed.split2061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2062 0 1 2 100 hg38.150200.bed.split2062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2063 0 1 2 100 hg38.150200.bed.split2063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2064 0 1 2 100 hg38.150200.bed.split2064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2065 0 1 2 100 hg38.150200.bed.split2065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2066 0 1 2 100 hg38.150200.bed.split2066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2067 0 1 2 100 hg38.150200.bed.split2067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2068 0 1 2 100 hg38.150200.bed.split2068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2069 0 1 2 100 hg38.150200.bed.split2069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split207 0 1 2 100 hg38.150200.bed.split207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2070 0 1 2 100 hg38.150200.bed.split2070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2071 0 1 2 100 hg38.150200.bed.split2071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2072 0 1 2 100 hg38.150200.bed.split2072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2073 0 1 2 100 hg38.150200.bed.split2073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2074 0 1 2 100 hg38.150200.bed.split2074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2075 0 1 2 100 hg38.150200.bed.split2075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2076 0 1 2 100 hg38.150200.bed.split2076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2077 0 1 2 100 hg38.150200.bed.split2077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2078 0 1 2 100 hg38.150200.bed.split2078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2079 0 1 2 100 hg38.150200.bed.split2079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split208 0 1 2 100 hg38.150200.bed.split208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2080 0 1 2 100 hg38.150200.bed.split2080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2081 0 1 2 100 hg38.150200.bed.split2081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2082 0 1 2 100 hg38.150200.bed.split2082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2083 0 1 2 100 hg38.150200.bed.split2083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2084 0 1 2 100 hg38.150200.bed.split2084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2085 0 1 2 100 hg38.150200.bed.split2085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2086 0 1 2 100 hg38.150200.bed.split2086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2087 0 1 2 100 hg38.150200.bed.split2087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2088 0 1 2 100 hg38.150200.bed.split2088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2089 0 1 2 100 hg38.150200.bed.split2089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split209 0 1 2 100 hg38.150200.bed.split209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2090 0 1 2 100 hg38.150200.bed.split2090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2091 0 1 2 100 hg38.150200.bed.split2091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2092 0 1 2 100 hg38.150200.bed.split2092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2093 0 1 2 100 hg38.150200.bed.split2093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2094 0 1 2 100 hg38.150200.bed.split2094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2095 0 1 2 100 hg38.150200.bed.split2095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2096 0 1 2 100 hg38.150200.bed.split2096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2097 0 1 2 100 hg38.150200.bed.split2097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2098 0 1 2 100 hg38.150200.bed.split2098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2099 0 1 2 100 hg38.150200.bed.split2099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split21 0 1 2 100 hg38.150200.bed.split21.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split210 0 1 2 100 hg38.150200.bed.split210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2100 0 1 2 100 hg38.150200.bed.split2100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2101 0 1 2 100 hg38.150200.bed.split2101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2102 0 1 2 100 hg38.150200.bed.split2102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2103 0 1 2 100 hg38.150200.bed.split2103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2104 0 1 2 100 hg38.150200.bed.split2104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2105 0 1 2 100 hg38.150200.bed.split2105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2106 0 1 2 100 hg38.150200.bed.split2106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2107 0 1 2 100 hg38.150200.bed.split2107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2108 0 1 2 100 hg38.150200.bed.split2108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2109 0 1 2 100 hg38.150200.bed.split2109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split211 0 1 2 100 hg38.150200.bed.split211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2110 0 1 2 100 hg38.150200.bed.split2110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2111 0 1 2 100 hg38.150200.bed.split2111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2112 0 1 2 100 hg38.150200.bed.split2112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2113 0 1 2 100 hg38.150200.bed.split2113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2114 0 1 2 100 hg38.150200.bed.split2114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2115 0 1 2 100 hg38.150200.bed.split2115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2116 0 1 2 100 hg38.150200.bed.split2116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2117 0 1 2 100 hg38.150200.bed.split2117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2118 0 1 2 100 hg38.150200.bed.split2118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2119 0 1 2 100 hg38.150200.bed.split2119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split212 0 1 2 100 hg38.150200.bed.split212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2120 0 1 2 100 hg38.150200.bed.split2120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2121 0 1 2 100 hg38.150200.bed.split2121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2122 0 1 2 100 hg38.150200.bed.split2122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2123 0 1 2 100 hg38.150200.bed.split2123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2124 0 1 2 100 hg38.150200.bed.split2124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2125 0 1 2 100 hg38.150200.bed.split2125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2126 0 1 2 100 hg38.150200.bed.split2126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2127 0 1 2 100 hg38.150200.bed.split2127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2128 0 1 2 100 hg38.150200.bed.split2128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2129 0 1 2 100 hg38.150200.bed.split2129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split213 0 1 2 100 hg38.150200.bed.split213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2130 0 1 2 100 hg38.150200.bed.split2130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2131 0 1 2 100 hg38.150200.bed.split2131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2132 0 1 2 100 hg38.150200.bed.split2132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2133 0 1 2 100 hg38.150200.bed.split2133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2134 0 1 2 100 hg38.150200.bed.split2134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2135 0 1 2 100 hg38.150200.bed.split2135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2136 0 1 2 100 hg38.150200.bed.split2136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2137 0 1 2 100 hg38.150200.bed.split2137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2138 0 1 2 100 hg38.150200.bed.split2138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2139 0 1 2 100 hg38.150200.bed.split2139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split214 0 1 2 100 hg38.150200.bed.split214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2140 0 1 2 100 hg38.150200.bed.split2140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2141 0 1 2 100 hg38.150200.bed.split2141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2142 0 1 2 100 hg38.150200.bed.split2142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2143 0 1 2 100 hg38.150200.bed.split2143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2144 0 1 2 100 hg38.150200.bed.split2144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2145 0 1 2 100 hg38.150200.bed.split2145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2146 0 1 2 100 hg38.150200.bed.split2146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2147 0 1 2 100 hg38.150200.bed.split2147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2148 0 1 2 100 hg38.150200.bed.split2148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2149 0 1 2 100 hg38.150200.bed.split2149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split215 0 1 2 100 hg38.150200.bed.split215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2150 0 1 2 100 hg38.150200.bed.split2150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2151 0 1 2 100 hg38.150200.bed.split2151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2152 0 1 2 100 hg38.150200.bed.split2152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2153 0 1 2 100 hg38.150200.bed.split2153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2154 0 1 2 100 hg38.150200.bed.split2154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2155 0 1 2 100 hg38.150200.bed.split2155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2156 0 1 2 100 hg38.150200.bed.split2156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2157 0 1 2 100 hg38.150200.bed.split2157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2158 0 1 2 100 hg38.150200.bed.split2158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2159 0 1 2 100 hg38.150200.bed.split2159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split216 0 1 2 100 hg38.150200.bed.split216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2160 0 1 2 100 hg38.150200.bed.split2160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2161 0 1 2 100 hg38.150200.bed.split2161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2162 0 1 2 100 hg38.150200.bed.split2162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2163 0 1 2 100 hg38.150200.bed.split2163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2164 0 1 2 100 hg38.150200.bed.split2164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2165 0 1 2 100 hg38.150200.bed.split2165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2166 0 1 2 100 hg38.150200.bed.split2166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2167 0 1 2 100 hg38.150200.bed.split2167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2168 0 1 2 100 hg38.150200.bed.split2168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2169 0 1 2 100 hg38.150200.bed.split2169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split217 0 1 2 100 hg38.150200.bed.split217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2170 0 1 2 100 hg38.150200.bed.split2170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2171 0 1 2 100 hg38.150200.bed.split2171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2172 0 1 2 100 hg38.150200.bed.split2172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2173 0 1 2 100 hg38.150200.bed.split2173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2174 0 1 2 100 hg38.150200.bed.split2174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2175 0 1 2 100 hg38.150200.bed.split2175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2176 0 1 2 100 hg38.150200.bed.split2176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2177 0 1 2 100 hg38.150200.bed.split2177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2178 0 1 2 100 hg38.150200.bed.split2178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2179 0 1 2 100 hg38.150200.bed.split2179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split218 0 1 2 100 hg38.150200.bed.split218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2180 0 1 2 100 hg38.150200.bed.split2180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2181 0 1 2 100 hg38.150200.bed.split2181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2182 0 1 2 100 hg38.150200.bed.split2182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2183 0 1 2 100 hg38.150200.bed.split2183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2184 0 1 2 100 hg38.150200.bed.split2184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2185 0 1 2 100 hg38.150200.bed.split2185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2186 0 1 2 100 hg38.150200.bed.split2186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2187 0 1 2 100 hg38.150200.bed.split2187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2188 0 1 2 100 hg38.150200.bed.split2188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2189 0 1 2 100 hg38.150200.bed.split2189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split219 0 1 2 100 hg38.150200.bed.split219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2190 0 1 2 100 hg38.150200.bed.split2190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2191 0 1 2 100 hg38.150200.bed.split2191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2192 0 1 2 100 hg38.150200.bed.split2192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2193 0 1 2 100 hg38.150200.bed.split2193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2194 0 1 2 100 hg38.150200.bed.split2194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2195 0 1 2 100 hg38.150200.bed.split2195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2196 0 1 2 100 hg38.150200.bed.split2196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2197 0 1 2 100 hg38.150200.bed.split2197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2198 0 1 2 100 hg38.150200.bed.split2198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2199 0 1 2 100 hg38.150200.bed.split2199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split22 0 1 2 100 hg38.150200.bed.split22.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split220 0 1 2 100 hg38.150200.bed.split220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2200 0 1 2 100 hg38.150200.bed.split2200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2201 0 1 2 100 hg38.150200.bed.split2201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2202 0 1 2 100 hg38.150200.bed.split2202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2203 0 1 2 100 hg38.150200.bed.split2203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2204 0 1 2 100 hg38.150200.bed.split2204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2205 0 1 2 100 hg38.150200.bed.split2205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2206 0 1 2 100 hg38.150200.bed.split2206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2207 0 1 2 100 hg38.150200.bed.split2207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2208 0 1 2 100 hg38.150200.bed.split2208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2209 0 1 2 100 hg38.150200.bed.split2209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split221 0 1 2 100 hg38.150200.bed.split221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2210 0 1 2 100 hg38.150200.bed.split2210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2211 0 1 2 100 hg38.150200.bed.split2211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2212 0 1 2 100 hg38.150200.bed.split2212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2213 0 1 2 100 hg38.150200.bed.split2213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2214 0 1 2 100 hg38.150200.bed.split2214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2215 0 1 2 100 hg38.150200.bed.split2215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2216 0 1 2 100 hg38.150200.bed.split2216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2217 0 1 2 100 hg38.150200.bed.split2217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2218 0 1 2 100 hg38.150200.bed.split2218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2219 0 1 2 100 hg38.150200.bed.split2219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split222 0 1 2 100 hg38.150200.bed.split222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2220 0 1 2 100 hg38.150200.bed.split2220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2221 0 1 2 100 hg38.150200.bed.split2221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2222 0 1 2 100 hg38.150200.bed.split2222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2223 0 1 2 100 hg38.150200.bed.split2223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2224 0 1 2 100 hg38.150200.bed.split2224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2225 0 1 2 100 hg38.150200.bed.split2225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2226 0 1 2 100 hg38.150200.bed.split2226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2227 0 1 2 100 hg38.150200.bed.split2227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2228 0 1 2 100 hg38.150200.bed.split2228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2229 0 1 2 100 hg38.150200.bed.split2229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split223 0 1 2 100 hg38.150200.bed.split223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2230 0 1 2 100 hg38.150200.bed.split2230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2231 0 1 2 100 hg38.150200.bed.split2231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2232 0 1 2 100 hg38.150200.bed.split2232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2233 0 1 2 100 hg38.150200.bed.split2233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2234 0 1 2 100 hg38.150200.bed.split2234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2235 0 1 2 100 hg38.150200.bed.split2235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2236 0 1 2 100 hg38.150200.bed.split2236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2237 0 1 2 100 hg38.150200.bed.split2237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2238 0 1 2 100 hg38.150200.bed.split2238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2239 0 1 2 100 hg38.150200.bed.split2239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split224 0 1 2 100 hg38.150200.bed.split224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2240 0 1 2 100 hg38.150200.bed.split2240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2241 0 1 2 100 hg38.150200.bed.split2241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2242 0 1 2 100 hg38.150200.bed.split2242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2243 0 1 2 100 hg38.150200.bed.split2243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2244 0 1 2 100 hg38.150200.bed.split2244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2245 0 1 2 100 hg38.150200.bed.split2245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2246 0 1 2 100 hg38.150200.bed.split2246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2247 0 1 2 100 hg38.150200.bed.split2247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2248 0 1 2 100 hg38.150200.bed.split2248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2249 0 1 2 100 hg38.150200.bed.split2249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split225 0 1 2 100 hg38.150200.bed.split225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2250 0 1 2 100 hg38.150200.bed.split2250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2251 0 1 2 100 hg38.150200.bed.split2251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2252 0 1 2 100 hg38.150200.bed.split2252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2253 0 1 2 100 hg38.150200.bed.split2253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2254 0 1 2 100 hg38.150200.bed.split2254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2255 0 1 2 100 hg38.150200.bed.split2255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2256 0 1 2 100 hg38.150200.bed.split2256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2257 0 1 2 100 hg38.150200.bed.split2257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2258 0 1 2 100 hg38.150200.bed.split2258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2259 0 1 2 100 hg38.150200.bed.split2259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split226 0 1 2 100 hg38.150200.bed.split226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2260 0 1 2 100 hg38.150200.bed.split2260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2261 0 1 2 100 hg38.150200.bed.split2261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2262 0 1 2 100 hg38.150200.bed.split2262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2263 0 1 2 100 hg38.150200.bed.split2263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2264 0 1 2 100 hg38.150200.bed.split2264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2265 0 1 2 100 hg38.150200.bed.split2265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2266 0 1 2 100 hg38.150200.bed.split2266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2267 0 1 2 100 hg38.150200.bed.split2267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2268 0 1 2 100 hg38.150200.bed.split2268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2269 0 1 2 100 hg38.150200.bed.split2269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split227 0 1 2 100 hg38.150200.bed.split227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2270 0 1 2 100 hg38.150200.bed.split2270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2271 0 1 2 100 hg38.150200.bed.split2271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2272 0 1 2 100 hg38.150200.bed.split2272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2273 0 1 2 100 hg38.150200.bed.split2273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2274 0 1 2 100 hg38.150200.bed.split2274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2275 0 1 2 100 hg38.150200.bed.split2275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2276 0 1 2 100 hg38.150200.bed.split2276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2277 0 1 2 100 hg38.150200.bed.split2277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2278 0 1 2 100 hg38.150200.bed.split2278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2279 0 1 2 100 hg38.150200.bed.split2279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split228 0 1 2 100 hg38.150200.bed.split228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2280 0 1 2 100 hg38.150200.bed.split2280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2281 0 1 2 100 hg38.150200.bed.split2281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2282 0 1 2 100 hg38.150200.bed.split2282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2283 0 1 2 100 hg38.150200.bed.split2283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2284 0 1 2 100 hg38.150200.bed.split2284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2285 0 1 2 100 hg38.150200.bed.split2285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2286 0 1 2 100 hg38.150200.bed.split2286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2287 0 1 2 100 hg38.150200.bed.split2287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2288 0 1 2 100 hg38.150200.bed.split2288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2289 0 1 2 100 hg38.150200.bed.split2289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split229 0 1 2 100 hg38.150200.bed.split229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2290 0 1 2 100 hg38.150200.bed.split2290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2291 0 1 2 100 hg38.150200.bed.split2291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2292 0 1 2 100 hg38.150200.bed.split2292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2293 0 1 2 100 hg38.150200.bed.split2293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2294 0 1 2 100 hg38.150200.bed.split2294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2295 0 1 2 100 hg38.150200.bed.split2295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2296 0 1 2 100 hg38.150200.bed.split2296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2297 0 1 2 100 hg38.150200.bed.split2297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2298 0 1 2 100 hg38.150200.bed.split2298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2299 0 1 2 100 hg38.150200.bed.split2299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split23 0 1 2 100 hg38.150200.bed.split23.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split230 0 1 2 100 hg38.150200.bed.split230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2300 0 1 2 100 hg38.150200.bed.split2300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2301 0 1 2 100 hg38.150200.bed.split2301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2302 0 1 2 100 hg38.150200.bed.split2302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2303 0 1 2 100 hg38.150200.bed.split2303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2304 0 1 2 100 hg38.150200.bed.split2304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2305 0 1 2 100 hg38.150200.bed.split2305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2306 0 1 2 100 hg38.150200.bed.split2306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2307 0 1 2 100 hg38.150200.bed.split2307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2308 0 1 2 100 hg38.150200.bed.split2308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2309 0 1 2 100 hg38.150200.bed.split2309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split231 0 1 2 100 hg38.150200.bed.split231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2310 0 1 2 100 hg38.150200.bed.split2310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2311 0 1 2 100 hg38.150200.bed.split2311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2312 0 1 2 100 hg38.150200.bed.split2312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2313 0 1 2 100 hg38.150200.bed.split2313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2314 0 1 2 100 hg38.150200.bed.split2314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2315 0 1 2 100 hg38.150200.bed.split2315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2316 0 1 2 100 hg38.150200.bed.split2316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2317 0 1 2 100 hg38.150200.bed.split2317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2318 0 1 2 100 hg38.150200.bed.split2318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2319 0 1 2 100 hg38.150200.bed.split2319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split232 0 1 2 100 hg38.150200.bed.split232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2320 0 1 2 100 hg38.150200.bed.split2320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2321 0 1 2 100 hg38.150200.bed.split2321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2322 0 1 2 100 hg38.150200.bed.split2322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2323 0 1 2 100 hg38.150200.bed.split2323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2324 0 1 2 100 hg38.150200.bed.split2324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2325 0 1 2 100 hg38.150200.bed.split2325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2326 0 1 2 100 hg38.150200.bed.split2326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2327 0 1 2 100 hg38.150200.bed.split2327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2328 0 1 2 100 hg38.150200.bed.split2328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2329 0 1 2 100 hg38.150200.bed.split2329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split233 0 1 2 100 hg38.150200.bed.split233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2330 0 1 2 100 hg38.150200.bed.split2330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2331 0 1 2 100 hg38.150200.bed.split2331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2332 0 1 2 100 hg38.150200.bed.split2332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2333 0 1 2 100 hg38.150200.bed.split2333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2334 0 1 2 100 hg38.150200.bed.split2334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2335 0 1 2 100 hg38.150200.bed.split2335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2336 0 1 2 100 hg38.150200.bed.split2336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2337 0 1 2 100 hg38.150200.bed.split2337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2338 0 1 2 100 hg38.150200.bed.split2338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2339 0 1 2 100 hg38.150200.bed.split2339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split234 0 1 2 100 hg38.150200.bed.split234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2340 0 1 2 100 hg38.150200.bed.split2340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2341 0 1 2 100 hg38.150200.bed.split2341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2342 0 1 2 100 hg38.150200.bed.split2342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2343 0 1 2 100 hg38.150200.bed.split2343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2344 0 1 2 100 hg38.150200.bed.split2344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2345 0 1 2 100 hg38.150200.bed.split2345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2346 0 1 2 100 hg38.150200.bed.split2346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2347 0 1 2 100 hg38.150200.bed.split2347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2348 0 1 2 100 hg38.150200.bed.split2348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2349 0 1 2 100 hg38.150200.bed.split2349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split235 0 1 2 100 hg38.150200.bed.split235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2350 0 1 2 100 hg38.150200.bed.split2350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2351 0 1 2 100 hg38.150200.bed.split2351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2352 0 1 2 100 hg38.150200.bed.split2352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2353 0 1 2 100 hg38.150200.bed.split2353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2354 0 1 2 100 hg38.150200.bed.split2354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2355 0 1 2 100 hg38.150200.bed.split2355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2356 0 1 2 100 hg38.150200.bed.split2356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2357 0 1 2 100 hg38.150200.bed.split2357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2358 0 1 2 100 hg38.150200.bed.split2358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2359 0 1 2 100 hg38.150200.bed.split2359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split236 0 1 2 100 hg38.150200.bed.split236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2360 0 1 2 100 hg38.150200.bed.split2360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2361 0 1 2 100 hg38.150200.bed.split2361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2362 0 1 2 100 hg38.150200.bed.split2362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2363 0 1 2 100 hg38.150200.bed.split2363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2364 0 1 2 100 hg38.150200.bed.split2364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2365 0 1 2 100 hg38.150200.bed.split2365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2366 0 1 2 100 hg38.150200.bed.split2366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2367 0 1 2 100 hg38.150200.bed.split2367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2368 0 1 2 100 hg38.150200.bed.split2368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2369 0 1 2 100 hg38.150200.bed.split2369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split237 0 1 2 100 hg38.150200.bed.split237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2370 0 1 2 100 hg38.150200.bed.split2370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2371 0 1 2 100 hg38.150200.bed.split2371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2372 0 1 2 100 hg38.150200.bed.split2372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2373 0 1 2 100 hg38.150200.bed.split2373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2374 0 1 2 100 hg38.150200.bed.split2374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2375 0 1 2 100 hg38.150200.bed.split2375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2376 0 1 2 100 hg38.150200.bed.split2376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2377 0 1 2 100 hg38.150200.bed.split2377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2378 0 1 2 100 hg38.150200.bed.split2378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2379 0 1 2 100 hg38.150200.bed.split2379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split238 0 1 2 100 hg38.150200.bed.split238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2380 0 1 2 100 hg38.150200.bed.split2380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2381 0 1 2 100 hg38.150200.bed.split2381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2382 0 1 2 100 hg38.150200.bed.split2382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2383 0 1 2 100 hg38.150200.bed.split2383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2384 0 1 2 100 hg38.150200.bed.split2384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2385 0 1 2 100 hg38.150200.bed.split2385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2386 0 1 2 100 hg38.150200.bed.split2386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2387 0 1 2 100 hg38.150200.bed.split2387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2388 0 1 2 100 hg38.150200.bed.split2388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2389 0 1 2 100 hg38.150200.bed.split2389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split239 0 1 2 100 hg38.150200.bed.split239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2390 0 1 2 100 hg38.150200.bed.split2390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2391 0 1 2 100 hg38.150200.bed.split2391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2392 0 1 2 100 hg38.150200.bed.split2392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2393 0 1 2 100 hg38.150200.bed.split2393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2394 0 1 2 100 hg38.150200.bed.split2394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2395 0 1 2 100 hg38.150200.bed.split2395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2396 0 1 2 100 hg38.150200.bed.split2396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2397 0 1 2 100 hg38.150200.bed.split2397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2398 0 1 2 100 hg38.150200.bed.split2398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2399 0 1 2 100 hg38.150200.bed.split2399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split24 0 1 2 100 hg38.150200.bed.split24.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split240 0 1 2 100 hg38.150200.bed.split240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2400 0 1 2 100 hg38.150200.bed.split2400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2401 0 1 2 100 hg38.150200.bed.split2401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2402 0 1 2 100 hg38.150200.bed.split2402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2403 0 1 2 100 hg38.150200.bed.split2403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2404 0 1 2 100 hg38.150200.bed.split2404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2405 0 1 2 100 hg38.150200.bed.split2405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2406 0 1 2 100 hg38.150200.bed.split2406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2407 0 1 2 100 hg38.150200.bed.split2407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2408 0 1 2 100 hg38.150200.bed.split2408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2409 0 1 2 100 hg38.150200.bed.split2409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split241 0 1 2 100 hg38.150200.bed.split241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2410 0 1 2 100 hg38.150200.bed.split2410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2411 0 1 2 100 hg38.150200.bed.split2411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2412 0 1 2 100 hg38.150200.bed.split2412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2413 0 1 2 100 hg38.150200.bed.split2413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2414 0 1 2 100 hg38.150200.bed.split2414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2415 0 1 2 100 hg38.150200.bed.split2415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2416 0 1 2 100 hg38.150200.bed.split2416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2417 0 1 2 100 hg38.150200.bed.split2417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2418 0 1 2 100 hg38.150200.bed.split2418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2419 0 1 2 100 hg38.150200.bed.split2419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split242 0 1 2 100 hg38.150200.bed.split242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2420 0 1 2 100 hg38.150200.bed.split2420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2421 0 1 2 100 hg38.150200.bed.split2421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2422 0 1 2 100 hg38.150200.bed.split2422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2423 0 1 2 100 hg38.150200.bed.split2423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2424 0 1 2 100 hg38.150200.bed.split2424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2425 0 1 2 100 hg38.150200.bed.split2425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2426 0 1 2 100 hg38.150200.bed.split2426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2427 0 1 2 100 hg38.150200.bed.split2427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2428 0 1 2 100 hg38.150200.bed.split2428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2429 0 1 2 100 hg38.150200.bed.split2429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split243 0 1 2 100 hg38.150200.bed.split243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2430 0 1 2 100 hg38.150200.bed.split2430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2431 0 1 2 100 hg38.150200.bed.split2431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2432 0 1 2 100 hg38.150200.bed.split2432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2433 0 1 2 100 hg38.150200.bed.split2433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2434 0 1 2 100 hg38.150200.bed.split2434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2435 0 1 2 100 hg38.150200.bed.split2435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2436 0 1 2 100 hg38.150200.bed.split2436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2437 0 1 2 100 hg38.150200.bed.split2437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2438 0 1 2 100 hg38.150200.bed.split2438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2439 0 1 2 100 hg38.150200.bed.split2439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split244 0 1 2 100 hg38.150200.bed.split244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2440 0 1 2 100 hg38.150200.bed.split2440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2441 0 1 2 100 hg38.150200.bed.split2441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2442 0 1 2 100 hg38.150200.bed.split2442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2443 0 1 2 100 hg38.150200.bed.split2443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2444 0 1 2 100 hg38.150200.bed.split2444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2445 0 1 2 100 hg38.150200.bed.split2445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2446 0 1 2 100 hg38.150200.bed.split2446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2447 0 1 2 100 hg38.150200.bed.split2447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2448 0 1 2 100 hg38.150200.bed.split2448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2449 0 1 2 100 hg38.150200.bed.split2449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split245 0 1 2 100 hg38.150200.bed.split245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2450 0 1 2 100 hg38.150200.bed.split2450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2451 0 1 2 100 hg38.150200.bed.split2451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2452 0 1 2 100 hg38.150200.bed.split2452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2453 0 1 2 100 hg38.150200.bed.split2453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2454 0 1 2 100 hg38.150200.bed.split2454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2455 0 1 2 100 hg38.150200.bed.split2455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2456 0 1 2 100 hg38.150200.bed.split2456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2457 0 1 2 100 hg38.150200.bed.split2457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2458 0 1 2 100 hg38.150200.bed.split2458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2459 0 1 2 100 hg38.150200.bed.split2459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split246 0 1 2 100 hg38.150200.bed.split246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2460 0 1 2 100 hg38.150200.bed.split2460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2461 0 1 2 100 hg38.150200.bed.split2461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2462 0 1 2 100 hg38.150200.bed.split2462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2463 0 1 2 100 hg38.150200.bed.split2463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2464 0 1 2 100 hg38.150200.bed.split2464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2465 0 1 2 100 hg38.150200.bed.split2465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2466 0 1 2 100 hg38.150200.bed.split2466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2467 0 1 2 100 hg38.150200.bed.split2467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2468 0 1 2 100 hg38.150200.bed.split2468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2469 0 1 2 100 hg38.150200.bed.split2469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split247 0 1 2 100 hg38.150200.bed.split247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2470 0 1 2 100 hg38.150200.bed.split2470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2471 0 1 2 100 hg38.150200.bed.split2471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2472 0 1 2 100 hg38.150200.bed.split2472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2473 0 1 2 100 hg38.150200.bed.split2473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2474 0 1 2 100 hg38.150200.bed.split2474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2475 0 1 2 100 hg38.150200.bed.split2475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2476 0 1 2 100 hg38.150200.bed.split2476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2477 0 1 2 100 hg38.150200.bed.split2477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2478 0 1 2 100 hg38.150200.bed.split2478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2479 0 1 2 100 hg38.150200.bed.split2479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split248 0 1 2 100 hg38.150200.bed.split248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2480 0 1 2 100 hg38.150200.bed.split2480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2481 0 1 2 100 hg38.150200.bed.split2481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2482 0 1 2 100 hg38.150200.bed.split2482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2483 0 1 2 100 hg38.150200.bed.split2483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2484 0 1 2 100 hg38.150200.bed.split2484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2485 0 1 2 100 hg38.150200.bed.split2485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2486 0 1 2 100 hg38.150200.bed.split2486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2487 0 1 2 100 hg38.150200.bed.split2487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2488 0 1 2 100 hg38.150200.bed.split2488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2489 0 1 2 100 hg38.150200.bed.split2489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split249 0 1 2 100 hg38.150200.bed.split249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2490 0 1 2 100 hg38.150200.bed.split2490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2491 0 1 2 100 hg38.150200.bed.split2491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2492 0 1 2 100 hg38.150200.bed.split2492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2493 0 1 2 100 hg38.150200.bed.split2493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2494 0 1 2 100 hg38.150200.bed.split2494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2495 0 1 2 100 hg38.150200.bed.split2495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2496 0 1 2 100 hg38.150200.bed.split2496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2497 0 1 2 100 hg38.150200.bed.split2497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2498 0 1 2 100 hg38.150200.bed.split2498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2499 0 1 2 100 hg38.150200.bed.split2499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split25 0 1 2 100 hg38.150200.bed.split25.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split250 0 1 2 100 hg38.150200.bed.split250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2500 0 1 2 100 hg38.150200.bed.split2500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2501 0 1 2 100 hg38.150200.bed.split2501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2502 0 1 2 100 hg38.150200.bed.split2502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2503 0 1 2 100 hg38.150200.bed.split2503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2504 0 1 2 100 hg38.150200.bed.split2504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2505 0 1 2 100 hg38.150200.bed.split2505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2506 0 1 2 100 hg38.150200.bed.split2506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2507 0 1 2 100 hg38.150200.bed.split2507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2508 0 1 2 100 hg38.150200.bed.split2508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2509 0 1 2 100 hg38.150200.bed.split2509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split251 0 1 2 100 hg38.150200.bed.split251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2510 0 1 2 100 hg38.150200.bed.split2510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2511 0 1 2 100 hg38.150200.bed.split2511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2512 0 1 2 100 hg38.150200.bed.split2512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2513 0 1 2 100 hg38.150200.bed.split2513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2514 0 1 2 100 hg38.150200.bed.split2514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2515 0 1 2 100 hg38.150200.bed.split2515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2516 0 1 2 100 hg38.150200.bed.split2516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2517 0 1 2 100 hg38.150200.bed.split2517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2518 0 1 2 100 hg38.150200.bed.split2518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2519 0 1 2 100 hg38.150200.bed.split2519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split252 0 1 2 100 hg38.150200.bed.split252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2520 0 1 2 100 hg38.150200.bed.split2520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2521 0 1 2 100 hg38.150200.bed.split2521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2522 0 1 2 100 hg38.150200.bed.split2522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2523 0 1 2 100 hg38.150200.bed.split2523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2524 0 1 2 100 hg38.150200.bed.split2524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2525 0 1 2 100 hg38.150200.bed.split2525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2526 0 1 2 100 hg38.150200.bed.split2526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2527 0 1 2 100 hg38.150200.bed.split2527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2528 0 1 2 100 hg38.150200.bed.split2528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2529 0 1 2 100 hg38.150200.bed.split2529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split253 0 1 2 100 hg38.150200.bed.split253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2530 0 1 2 100 hg38.150200.bed.split2530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2531 0 1 2 100 hg38.150200.bed.split2531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2532 0 1 2 100 hg38.150200.bed.split2532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2533 0 1 2 100 hg38.150200.bed.split2533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2534 0 1 2 100 hg38.150200.bed.split2534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2535 0 1 2 100 hg38.150200.bed.split2535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2536 0 1 2 100 hg38.150200.bed.split2536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2537 0 1 2 100 hg38.150200.bed.split2537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2538 0 1 2 100 hg38.150200.bed.split2538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2539 0 1 2 100 hg38.150200.bed.split2539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split254 0 1 2 100 hg38.150200.bed.split254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2540 0 1 2 100 hg38.150200.bed.split2540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2541 0 1 2 100 hg38.150200.bed.split2541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2542 0 1 2 100 hg38.150200.bed.split2542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2543 0 1 2 100 hg38.150200.bed.split2543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2544 0 1 2 100 hg38.150200.bed.split2544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2545 0 1 2 100 hg38.150200.bed.split2545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2546 0 1 2 100 hg38.150200.bed.split2546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2547 0 1 2 100 hg38.150200.bed.split2547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2548 0 1 2 100 hg38.150200.bed.split2548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2549 0 1 2 100 hg38.150200.bed.split2549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split255 0 1 2 100 hg38.150200.bed.split255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2550 0 1 2 100 hg38.150200.bed.split2550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2551 0 1 2 100 hg38.150200.bed.split2551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2552 0 1 2 100 hg38.150200.bed.split2552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2553 0 1 2 100 hg38.150200.bed.split2553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2554 0 1 2 100 hg38.150200.bed.split2554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2555 0 1 2 100 hg38.150200.bed.split2555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2556 0 1 2 100 hg38.150200.bed.split2556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2557 0 1 2 100 hg38.150200.bed.split2557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2558 0 1 2 100 hg38.150200.bed.split2558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2559 0 1 2 100 hg38.150200.bed.split2559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split256 0 1 2 100 hg38.150200.bed.split256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2560 0 1 2 100 hg38.150200.bed.split2560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2561 0 1 2 100 hg38.150200.bed.split2561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2562 0 1 2 100 hg38.150200.bed.split2562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2563 0 1 2 100 hg38.150200.bed.split2563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2564 0 1 2 100 hg38.150200.bed.split2564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2565 0 1 2 100 hg38.150200.bed.split2565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2566 0 1 2 100 hg38.150200.bed.split2566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2567 0 1 2 100 hg38.150200.bed.split2567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2568 0 1 2 100 hg38.150200.bed.split2568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2569 0 1 2 100 hg38.150200.bed.split2569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split257 0 1 2 100 hg38.150200.bed.split257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2570 0 1 2 100 hg38.150200.bed.split2570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2571 0 1 2 100 hg38.150200.bed.split2571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2572 0 1 2 100 hg38.150200.bed.split2572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2573 0 1 2 100 hg38.150200.bed.split2573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2574 0 1 2 100 hg38.150200.bed.split2574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2575 0 1 2 100 hg38.150200.bed.split2575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2576 0 1 2 100 hg38.150200.bed.split2576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2577 0 1 2 100 hg38.150200.bed.split2577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2578 0 1 2 100 hg38.150200.bed.split2578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2579 0 1 2 100 hg38.150200.bed.split2579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split258 0 1 2 100 hg38.150200.bed.split258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2580 0 1 2 100 hg38.150200.bed.split2580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2581 0 1 2 100 hg38.150200.bed.split2581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2582 0 1 2 100 hg38.150200.bed.split2582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2583 0 1 2 100 hg38.150200.bed.split2583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2584 0 1 2 100 hg38.150200.bed.split2584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2585 0 1 2 100 hg38.150200.bed.split2585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2586 0 1 2 100 hg38.150200.bed.split2586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2587 0 1 2 100 hg38.150200.bed.split2587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2588 0 1 2 100 hg38.150200.bed.split2588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2589 0 1 2 100 hg38.150200.bed.split2589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split259 0 1 2 100 hg38.150200.bed.split259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2590 0 1 2 100 hg38.150200.bed.split2590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2591 0 1 2 100 hg38.150200.bed.split2591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2592 0 1 2 100 hg38.150200.bed.split2592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2593 0 1 2 100 hg38.150200.bed.split2593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2594 0 1 2 100 hg38.150200.bed.split2594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2595 0 1 2 100 hg38.150200.bed.split2595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2596 0 1 2 100 hg38.150200.bed.split2596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2597 0 1 2 100 hg38.150200.bed.split2597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2598 0 1 2 100 hg38.150200.bed.split2598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2599 0 1 2 100 hg38.150200.bed.split2599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split26 0 1 2 100 hg38.150200.bed.split26.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split260 0 1 2 100 hg38.150200.bed.split260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2600 0 1 2 100 hg38.150200.bed.split2600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2601 0 1 2 100 hg38.150200.bed.split2601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2602 0 1 2 100 hg38.150200.bed.split2602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2603 0 1 2 100 hg38.150200.bed.split2603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2604 0 1 2 100 hg38.150200.bed.split2604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2605 0 1 2 100 hg38.150200.bed.split2605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2606 0 1 2 100 hg38.150200.bed.split2606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2607 0 1 2 100 hg38.150200.bed.split2607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2608 0 1 2 100 hg38.150200.bed.split2608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2609 0 1 2 100 hg38.150200.bed.split2609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split261 0 1 2 100 hg38.150200.bed.split261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2610 0 1 2 100 hg38.150200.bed.split2610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2611 0 1 2 100 hg38.150200.bed.split2611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2612 0 1 2 100 hg38.150200.bed.split2612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2613 0 1 2 100 hg38.150200.bed.split2613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2614 0 1 2 100 hg38.150200.bed.split2614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2615 0 1 2 100 hg38.150200.bed.split2615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2616 0 1 2 100 hg38.150200.bed.split2616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2617 0 1 2 100 hg38.150200.bed.split2617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2618 0 1 2 100 hg38.150200.bed.split2618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2619 0 1 2 100 hg38.150200.bed.split2619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split262 0 1 2 100 hg38.150200.bed.split262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2620 0 1 2 100 hg38.150200.bed.split2620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2621 0 1 2 100 hg38.150200.bed.split2621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2622 0 1 2 100 hg38.150200.bed.split2622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2623 0 1 2 100 hg38.150200.bed.split2623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2624 0 1 2 100 hg38.150200.bed.split2624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2625 0 1 2 100 hg38.150200.bed.split2625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2626 0 1 2 100 hg38.150200.bed.split2626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2627 0 1 2 100 hg38.150200.bed.split2627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2628 0 1 2 100 hg38.150200.bed.split2628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2629 0 1 2 100 hg38.150200.bed.split2629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split263 0 1 2 100 hg38.150200.bed.split263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2630 0 1 2 100 hg38.150200.bed.split2630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2631 0 1 2 100 hg38.150200.bed.split2631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2632 0 1 2 100 hg38.150200.bed.split2632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2633 0 1 2 100 hg38.150200.bed.split2633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2634 0 1 2 100 hg38.150200.bed.split2634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2635 0 1 2 100 hg38.150200.bed.split2635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2636 0 1 2 100 hg38.150200.bed.split2636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2637 0 1 2 100 hg38.150200.bed.split2637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2638 0 1 2 100 hg38.150200.bed.split2638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2639 0 1 2 100 hg38.150200.bed.split2639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split264 0 1 2 100 hg38.150200.bed.split264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2640 0 1 2 100 hg38.150200.bed.split2640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2641 0 1 2 100 hg38.150200.bed.split2641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2642 0 1 2 100 hg38.150200.bed.split2642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2643 0 1 2 100 hg38.150200.bed.split2643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2644 0 1 2 100 hg38.150200.bed.split2644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2645 0 1 2 100 hg38.150200.bed.split2645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2646 0 1 2 100 hg38.150200.bed.split2646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2647 0 1 2 100 hg38.150200.bed.split2647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2648 0 1 2 100 hg38.150200.bed.split2648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2649 0 1 2 100 hg38.150200.bed.split2649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split265 0 1 2 100 hg38.150200.bed.split265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2650 0 1 2 100 hg38.150200.bed.split2650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2651 0 1 2 100 hg38.150200.bed.split2651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2652 0 1 2 100 hg38.150200.bed.split2652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2653 0 1 2 100 hg38.150200.bed.split2653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2654 0 1 2 100 hg38.150200.bed.split2654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2655 0 1 2 100 hg38.150200.bed.split2655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2656 0 1 2 100 hg38.150200.bed.split2656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2657 0 1 2 100 hg38.150200.bed.split2657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2658 0 1 2 100 hg38.150200.bed.split2658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2659 0 1 2 100 hg38.150200.bed.split2659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split266 0 1 2 100 hg38.150200.bed.split266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2660 0 1 2 100 hg38.150200.bed.split2660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2661 0 1 2 100 hg38.150200.bed.split2661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2662 0 1 2 100 hg38.150200.bed.split2662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2663 0 1 2 100 hg38.150200.bed.split2663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2664 0 1 2 100 hg38.150200.bed.split2664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2665 0 1 2 100 hg38.150200.bed.split2665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2666 0 1 2 100 hg38.150200.bed.split2666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2667 0 1 2 100 hg38.150200.bed.split2667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2668 0 1 2 100 hg38.150200.bed.split2668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2669 0 1 2 100 hg38.150200.bed.split2669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split267 0 1 2 100 hg38.150200.bed.split267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2670 0 1 2 100 hg38.150200.bed.split2670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2671 0 1 2 100 hg38.150200.bed.split2671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2672 0 1 2 100 hg38.150200.bed.split2672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2673 0 1 2 100 hg38.150200.bed.split2673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2674 0 1 2 100 hg38.150200.bed.split2674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2675 0 1 2 100 hg38.150200.bed.split2675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2676 0 1 2 100 hg38.150200.bed.split2676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2677 0 1 2 100 hg38.150200.bed.split2677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2678 0 1 2 100 hg38.150200.bed.split2678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2679 0 1 2 100 hg38.150200.bed.split2679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split268 0 1 2 100 hg38.150200.bed.split268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2680 0 1 2 100 hg38.150200.bed.split2680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2681 0 1 2 100 hg38.150200.bed.split2681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2682 0 1 2 100 hg38.150200.bed.split2682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2683 0 1 2 100 hg38.150200.bed.split2683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2684 0 1 2 100 hg38.150200.bed.split2684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2685 0 1 2 100 hg38.150200.bed.split2685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2686 0 1 2 100 hg38.150200.bed.split2686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2687 0 1 2 100 hg38.150200.bed.split2687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2688 0 1 2 100 hg38.150200.bed.split2688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2689 0 1 2 100 hg38.150200.bed.split2689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split269 0 1 2 100 hg38.150200.bed.split269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2690 0 1 2 100 hg38.150200.bed.split2690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2691 0 1 2 100 hg38.150200.bed.split2691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2692 0 1 2 100 hg38.150200.bed.split2692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2693 0 1 2 100 hg38.150200.bed.split2693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2694 0 1 2 100 hg38.150200.bed.split2694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2695 0 1 2 100 hg38.150200.bed.split2695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2696 0 1 2 100 hg38.150200.bed.split2696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2697 0 1 2 100 hg38.150200.bed.split2697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2698 0 1 2 100 hg38.150200.bed.split2698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2699 0 1 2 100 hg38.150200.bed.split2699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split27 0 1 2 100 hg38.150200.bed.split27.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split270 0 1 2 100 hg38.150200.bed.split270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2700 0 1 2 100 hg38.150200.bed.split2700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2701 0 1 2 100 hg38.150200.bed.split2701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2702 0 1 2 100 hg38.150200.bed.split2702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2703 0 1 2 100 hg38.150200.bed.split2703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2704 0 1 2 100 hg38.150200.bed.split2704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2705 0 1 2 100 hg38.150200.bed.split2705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2706 0 1 2 100 hg38.150200.bed.split2706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2707 0 1 2 100 hg38.150200.bed.split2707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2708 0 1 2 100 hg38.150200.bed.split2708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2709 0 1 2 100 hg38.150200.bed.split2709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split271 0 1 2 100 hg38.150200.bed.split271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2710 0 1 2 100 hg38.150200.bed.split2710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2711 0 1 2 100 hg38.150200.bed.split2711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2712 0 1 2 100 hg38.150200.bed.split2712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2713 0 1 2 100 hg38.150200.bed.split2713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2714 0 1 2 100 hg38.150200.bed.split2714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2715 0 1 2 100 hg38.150200.bed.split2715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2716 0 1 2 100 hg38.150200.bed.split2716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2717 0 1 2 100 hg38.150200.bed.split2717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2718 0 1 2 100 hg38.150200.bed.split2718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2719 0 1 2 100 hg38.150200.bed.split2719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split272 0 1 2 100 hg38.150200.bed.split272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2720 0 1 2 100 hg38.150200.bed.split2720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2721 0 1 2 100 hg38.150200.bed.split2721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2722 0 1 2 100 hg38.150200.bed.split2722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2723 0 1 2 100 hg38.150200.bed.split2723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2724 0 1 2 100 hg38.150200.bed.split2724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2725 0 1 2 100 hg38.150200.bed.split2725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2726 0 1 2 100 hg38.150200.bed.split2726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2727 0 1 2 100 hg38.150200.bed.split2727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2728 0 1 2 100 hg38.150200.bed.split2728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2729 0 1 2 100 hg38.150200.bed.split2729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split273 0 1 2 100 hg38.150200.bed.split273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2730 0 1 2 100 hg38.150200.bed.split2730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2731 0 1 2 100 hg38.150200.bed.split2731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2732 0 1 2 100 hg38.150200.bed.split2732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2733 0 1 2 100 hg38.150200.bed.split2733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2734 0 1 2 100 hg38.150200.bed.split2734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2735 0 1 2 100 hg38.150200.bed.split2735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2736 0 1 2 100 hg38.150200.bed.split2736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2737 0 1 2 100 hg38.150200.bed.split2737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2738 0 1 2 100 hg38.150200.bed.split2738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2739 0 1 2 100 hg38.150200.bed.split2739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split274 0 1 2 100 hg38.150200.bed.split274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2740 0 1 2 100 hg38.150200.bed.split2740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2741 0 1 2 100 hg38.150200.bed.split2741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2742 0 1 2 100 hg38.150200.bed.split2742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2743 0 1 2 100 hg38.150200.bed.split2743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2744 0 1 2 100 hg38.150200.bed.split2744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2745 0 1 2 100 hg38.150200.bed.split2745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2746 0 1 2 100 hg38.150200.bed.split2746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2747 0 1 2 100 hg38.150200.bed.split2747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2748 0 1 2 100 hg38.150200.bed.split2748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2749 0 1 2 100 hg38.150200.bed.split2749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split275 0 1 2 100 hg38.150200.bed.split275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2750 0 1 2 100 hg38.150200.bed.split2750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2751 0 1 2 100 hg38.150200.bed.split2751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2752 0 1 2 100 hg38.150200.bed.split2752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2753 0 1 2 100 hg38.150200.bed.split2753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2754 0 1 2 100 hg38.150200.bed.split2754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2755 0 1 2 100 hg38.150200.bed.split2755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2756 0 1 2 100 hg38.150200.bed.split2756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2757 0 1 2 100 hg38.150200.bed.split2757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2758 0 1 2 100 hg38.150200.bed.split2758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2759 0 1 2 100 hg38.150200.bed.split2759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split276 0 1 2 100 hg38.150200.bed.split276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2760 0 1 2 100 hg38.150200.bed.split2760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2761 0 1 2 100 hg38.150200.bed.split2761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2762 0 1 2 100 hg38.150200.bed.split2762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2763 0 1 2 100 hg38.150200.bed.split2763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2764 0 1 2 100 hg38.150200.bed.split2764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2765 0 1 2 100 hg38.150200.bed.split2765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2766 0 1 2 100 hg38.150200.bed.split2766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2767 0 1 2 100 hg38.150200.bed.split2767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2768 0 1 2 100 hg38.150200.bed.split2768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2769 0 1 2 100 hg38.150200.bed.split2769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split277 0 1 2 100 hg38.150200.bed.split277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2770 0 1 2 100 hg38.150200.bed.split2770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2771 0 1 2 100 hg38.150200.bed.split2771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2772 0 1 2 100 hg38.150200.bed.split2772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2773 0 1 2 100 hg38.150200.bed.split2773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2774 0 1 2 100 hg38.150200.bed.split2774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2775 0 1 2 100 hg38.150200.bed.split2775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2776 0 1 2 100 hg38.150200.bed.split2776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2777 0 1 2 100 hg38.150200.bed.split2777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2778 0 1 2 100 hg38.150200.bed.split2778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2779 0 1 2 100 hg38.150200.bed.split2779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split278 0 1 2 100 hg38.150200.bed.split278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2780 0 1 2 100 hg38.150200.bed.split2780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2781 0 1 2 100 hg38.150200.bed.split2781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2782 0 1 2 100 hg38.150200.bed.split2782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2783 0 1 2 100 hg38.150200.bed.split2783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2784 0 1 2 100 hg38.150200.bed.split2784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2785 0 1 2 100 hg38.150200.bed.split2785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2786 0 1 2 100 hg38.150200.bed.split2786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2787 0 1 2 100 hg38.150200.bed.split2787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2788 0 1 2 100 hg38.150200.bed.split2788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2789 0 1 2 100 hg38.150200.bed.split2789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split279 0 1 2 100 hg38.150200.bed.split279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2790 0 1 2 100 hg38.150200.bed.split2790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2791 0 1 2 100 hg38.150200.bed.split2791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2792 0 1 2 100 hg38.150200.bed.split2792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2793 0 1 2 100 hg38.150200.bed.split2793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2794 0 1 2 100 hg38.150200.bed.split2794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2795 0 1 2 100 hg38.150200.bed.split2795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2796 0 1 2 100 hg38.150200.bed.split2796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2797 0 1 2 100 hg38.150200.bed.split2797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2798 0 1 2 100 hg38.150200.bed.split2798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2799 0 1 2 100 hg38.150200.bed.split2799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split28 0 1 2 100 hg38.150200.bed.split28.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split280 0 1 2 100 hg38.150200.bed.split280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2800 0 1 2 100 hg38.150200.bed.split2800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2801 0 1 2 100 hg38.150200.bed.split2801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2802 0 1 2 100 hg38.150200.bed.split2802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2803 0 1 2 100 hg38.150200.bed.split2803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2804 0 1 2 100 hg38.150200.bed.split2804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2805 0 1 2 100 hg38.150200.bed.split2805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2806 0 1 2 100 hg38.150200.bed.split2806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2807 0 1 2 100 hg38.150200.bed.split2807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2808 0 1 2 100 hg38.150200.bed.split2808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2809 0 1 2 100 hg38.150200.bed.split2809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split281 0 1 2 100 hg38.150200.bed.split281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2810 0 1 2 100 hg38.150200.bed.split2810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2811 0 1 2 100 hg38.150200.bed.split2811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2812 0 1 2 100 hg38.150200.bed.split2812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2813 0 1 2 100 hg38.150200.bed.split2813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2814 0 1 2 100 hg38.150200.bed.split2814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2815 0 1 2 100 hg38.150200.bed.split2815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2816 0 1 2 100 hg38.150200.bed.split2816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2817 0 1 2 100 hg38.150200.bed.split2817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2818 0 1 2 100 hg38.150200.bed.split2818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2819 0 1 2 100 hg38.150200.bed.split2819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split282 0 1 2 100 hg38.150200.bed.split282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2820 0 1 2 100 hg38.150200.bed.split2820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2821 0 1 2 100 hg38.150200.bed.split2821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2822 0 1 2 100 hg38.150200.bed.split2822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2823 0 1 2 100 hg38.150200.bed.split2823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2824 0 1 2 100 hg38.150200.bed.split2824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2825 0 1 2 100 hg38.150200.bed.split2825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2826 0 1 2 100 hg38.150200.bed.split2826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2827 0 1 2 100 hg38.150200.bed.split2827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2828 0 1 2 100 hg38.150200.bed.split2828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2829 0 1 2 100 hg38.150200.bed.split2829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split283 0 1 2 100 hg38.150200.bed.split283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2830 0 1 2 100 hg38.150200.bed.split2830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2831 0 1 2 100 hg38.150200.bed.split2831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2832 0 1 2 100 hg38.150200.bed.split2832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2833 0 1 2 100 hg38.150200.bed.split2833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2834 0 1 2 100 hg38.150200.bed.split2834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2835 0 1 2 100 hg38.150200.bed.split2835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2836 0 1 2 100 hg38.150200.bed.split2836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2837 0 1 2 100 hg38.150200.bed.split2837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2838 0 1 2 100 hg38.150200.bed.split2838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2839 0 1 2 100 hg38.150200.bed.split2839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split284 0 1 2 100 hg38.150200.bed.split284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2840 0 1 2 100 hg38.150200.bed.split2840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2841 0 1 2 100 hg38.150200.bed.split2841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2842 0 1 2 100 hg38.150200.bed.split2842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2843 0 1 2 100 hg38.150200.bed.split2843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2844 0 1 2 100 hg38.150200.bed.split2844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2845 0 1 2 100 hg38.150200.bed.split2845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2846 0 1 2 100 hg38.150200.bed.split2846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2847 0 1 2 100 hg38.150200.bed.split2847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2848 0 1 2 100 hg38.150200.bed.split2848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2849 0 1 2 100 hg38.150200.bed.split2849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split285 0 1 2 100 hg38.150200.bed.split285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2850 0 1 2 100 hg38.150200.bed.split2850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2851 0 1 2 100 hg38.150200.bed.split2851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2852 0 1 2 100 hg38.150200.bed.split2852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2853 0 1 2 100 hg38.150200.bed.split2853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2854 0 1 2 100 hg38.150200.bed.split2854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2855 0 1 2 100 hg38.150200.bed.split2855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2856 0 1 2 100 hg38.150200.bed.split2856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2857 0 1 2 100 hg38.150200.bed.split2857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2858 0 1 2 100 hg38.150200.bed.split2858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2859 0 1 2 100 hg38.150200.bed.split2859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split286 0 1 2 100 hg38.150200.bed.split286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2860 0 1 2 100 hg38.150200.bed.split2860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2861 0 1 2 100 hg38.150200.bed.split2861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2862 0 1 2 100 hg38.150200.bed.split2862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2863 0 1 2 100 hg38.150200.bed.split2863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2864 0 1 2 100 hg38.150200.bed.split2864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2865 0 1 2 100 hg38.150200.bed.split2865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2866 0 1 2 100 hg38.150200.bed.split2866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2867 0 1 2 100 hg38.150200.bed.split2867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2868 0 1 2 100 hg38.150200.bed.split2868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2869 0 1 2 100 hg38.150200.bed.split2869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split287 0 1 2 100 hg38.150200.bed.split287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2870 0 1 2 100 hg38.150200.bed.split2870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2871 0 1 2 100 hg38.150200.bed.split2871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2872 0 1 2 100 hg38.150200.bed.split2872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2873 0 1 2 100 hg38.150200.bed.split2873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2874 0 1 2 100 hg38.150200.bed.split2874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2875 0 1 2 100 hg38.150200.bed.split2875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2876 0 1 2 100 hg38.150200.bed.split2876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2877 0 1 2 100 hg38.150200.bed.split2877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2878 0 1 2 100 hg38.150200.bed.split2878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2879 0 1 2 100 hg38.150200.bed.split2879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split288 0 1 2 100 hg38.150200.bed.split288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2880 0 1 2 100 hg38.150200.bed.split2880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2881 0 1 2 100 hg38.150200.bed.split2881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2882 0 1 2 100 hg38.150200.bed.split2882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2883 0 1 2 100 hg38.150200.bed.split2883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2884 0 1 2 100 hg38.150200.bed.split2884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2885 0 1 2 100 hg38.150200.bed.split2885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2886 0 1 2 100 hg38.150200.bed.split2886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2887 0 1 2 100 hg38.150200.bed.split2887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2888 0 1 2 100 hg38.150200.bed.split2888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2889 0 1 2 100 hg38.150200.bed.split2889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split289 0 1 2 100 hg38.150200.bed.split289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2890 0 1 2 100 hg38.150200.bed.split2890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2891 0 1 2 100 hg38.150200.bed.split2891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2892 0 1 2 100 hg38.150200.bed.split2892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2893 0 1 2 100 hg38.150200.bed.split2893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2894 0 1 2 100 hg38.150200.bed.split2894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2895 0 1 2 100 hg38.150200.bed.split2895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2896 0 1 2 100 hg38.150200.bed.split2896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2897 0 1 2 100 hg38.150200.bed.split2897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2898 0 1 2 100 hg38.150200.bed.split2898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2899 0 1 2 100 hg38.150200.bed.split2899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split29 0 1 2 100 hg38.150200.bed.split29.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split290 0 1 2 100 hg38.150200.bed.split290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2900 0 1 2 100 hg38.150200.bed.split2900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2901 0 1 2 100 hg38.150200.bed.split2901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2902 0 1 2 100 hg38.150200.bed.split2902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2903 0 1 2 100 hg38.150200.bed.split2903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2904 0 1 2 100 hg38.150200.bed.split2904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2905 0 1 2 100 hg38.150200.bed.split2905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2906 0 1 2 100 hg38.150200.bed.split2906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2907 0 1 2 100 hg38.150200.bed.split2907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2908 0 1 2 100 hg38.150200.bed.split2908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2909 0 1 2 100 hg38.150200.bed.split2909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split291 0 1 2 100 hg38.150200.bed.split291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2910 0 1 2 100 hg38.150200.bed.split2910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2911 0 1 2 100 hg38.150200.bed.split2911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2912 0 1 2 100 hg38.150200.bed.split2912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2913 0 1 2 100 hg38.150200.bed.split2913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2914 0 1 2 100 hg38.150200.bed.split2914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2915 0 1 2 100 hg38.150200.bed.split2915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2916 0 1 2 100 hg38.150200.bed.split2916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2917 0 1 2 100 hg38.150200.bed.split2917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2918 0 1 2 100 hg38.150200.bed.split2918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2919 0 1 2 100 hg38.150200.bed.split2919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split292 0 1 2 100 hg38.150200.bed.split292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2920 0 1 2 100 hg38.150200.bed.split2920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2921 0 1 2 100 hg38.150200.bed.split2921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2922 0 1 2 100 hg38.150200.bed.split2922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2923 0 1 2 100 hg38.150200.bed.split2923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2924 0 1 2 100 hg38.150200.bed.split2924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2925 0 1 2 100 hg38.150200.bed.split2925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2926 0 1 2 100 hg38.150200.bed.split2926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2927 0 1 2 100 hg38.150200.bed.split2927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2928 0 1 2 100 hg38.150200.bed.split2928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2929 0 1 2 100 hg38.150200.bed.split2929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split293 0 1 2 100 hg38.150200.bed.split293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2930 0 1 2 100 hg38.150200.bed.split2930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2931 0 1 2 100 hg38.150200.bed.split2931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2932 0 1 2 100 hg38.150200.bed.split2932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2933 0 1 2 100 hg38.150200.bed.split2933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2934 0 1 2 100 hg38.150200.bed.split2934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2935 0 1 2 100 hg38.150200.bed.split2935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2936 0 1 2 100 hg38.150200.bed.split2936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2937 0 1 2 100 hg38.150200.bed.split2937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2938 0 1 2 100 hg38.150200.bed.split2938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2939 0 1 2 100 hg38.150200.bed.split2939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split294 0 1 2 100 hg38.150200.bed.split294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2940 0 1 2 100 hg38.150200.bed.split2940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2941 0 1 2 100 hg38.150200.bed.split2941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2942 0 1 2 100 hg38.150200.bed.split2942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2943 0 1 2 100 hg38.150200.bed.split2943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2944 0 1 2 100 hg38.150200.bed.split2944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2945 0 1 2 100 hg38.150200.bed.split2945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2946 0 1 2 100 hg38.150200.bed.split2946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2947 0 1 2 100 hg38.150200.bed.split2947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2948 0 1 2 100 hg38.150200.bed.split2948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2949 0 1 2 100 hg38.150200.bed.split2949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split295 0 1 2 100 hg38.150200.bed.split295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2950 0 1 2 100 hg38.150200.bed.split2950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2951 0 1 2 100 hg38.150200.bed.split2951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2952 0 1 2 100 hg38.150200.bed.split2952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2953 0 1 2 100 hg38.150200.bed.split2953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2954 0 1 2 100 hg38.150200.bed.split2954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2955 0 1 2 100 hg38.150200.bed.split2955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2956 0 1 2 100 hg38.150200.bed.split2956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2957 0 1 2 100 hg38.150200.bed.split2957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2958 0 1 2 100 hg38.150200.bed.split2958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2959 0 1 2 100 hg38.150200.bed.split2959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split296 0 1 2 100 hg38.150200.bed.split296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2960 0 1 2 100 hg38.150200.bed.split2960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2961 0 1 2 100 hg38.150200.bed.split2961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2962 0 1 2 100 hg38.150200.bed.split2962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2963 0 1 2 100 hg38.150200.bed.split2963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2964 0 1 2 100 hg38.150200.bed.split2964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2965 0 1 2 100 hg38.150200.bed.split2965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2966 0 1 2 100 hg38.150200.bed.split2966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2967 0 1 2 100 hg38.150200.bed.split2967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2968 0 1 2 100 hg38.150200.bed.split2968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2969 0 1 2 100 hg38.150200.bed.split2969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split297 0 1 2 100 hg38.150200.bed.split297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2970 0 1 2 100 hg38.150200.bed.split2970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2971 0 1 2 100 hg38.150200.bed.split2971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2972 0 1 2 100 hg38.150200.bed.split2972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2973 0 1 2 100 hg38.150200.bed.split2973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2974 0 1 2 100 hg38.150200.bed.split2974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2975 0 1 2 100 hg38.150200.bed.split2975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2976 0 1 2 100 hg38.150200.bed.split2976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2977 0 1 2 100 hg38.150200.bed.split2977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2978 0 1 2 100 hg38.150200.bed.split2978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2979 0 1 2 100 hg38.150200.bed.split2979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split298 0 1 2 100 hg38.150200.bed.split298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2980 0 1 2 100 hg38.150200.bed.split2980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2981 0 1 2 100 hg38.150200.bed.split2981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2982 0 1 2 100 hg38.150200.bed.split2982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2983 0 1 2 100 hg38.150200.bed.split2983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2984 0 1 2 100 hg38.150200.bed.split2984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2985 0 1 2 100 hg38.150200.bed.split2985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2986 0 1 2 100 hg38.150200.bed.split2986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2987 0 1 2 100 hg38.150200.bed.split2987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2988 0 1 2 100 hg38.150200.bed.split2988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2989 0 1 2 100 hg38.150200.bed.split2989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split299 0 1 2 100 hg38.150200.bed.split299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2990 0 1 2 100 hg38.150200.bed.split2990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2991 0 1 2 100 hg38.150200.bed.split2991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2992 0 1 2 100 hg38.150200.bed.split2992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2993 0 1 2 100 hg38.150200.bed.split2993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2994 0 1 2 100 hg38.150200.bed.split2994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2995 0 1 2 100 hg38.150200.bed.split2995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2996 0 1 2 100 hg38.150200.bed.split2996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2997 0 1 2 100 hg38.150200.bed.split2997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2998 0 1 2 100 hg38.150200.bed.split2998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split2999 0 1 2 100 hg38.150200.bed.split2999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3 0 1 2 100 hg38.150200.bed.split3.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split30 0 1 2 100 hg38.150200.bed.split30.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split300 0 1 2 100 hg38.150200.bed.split300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3000 0 1 2 100 hg38.150200.bed.split3000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3001 0 1 2 100 hg38.150200.bed.split3001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3002 0 1 2 100 hg38.150200.bed.split3002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3003 0 1 2 100 hg38.150200.bed.split3003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3004 0 1 2 100 hg38.150200.bed.split3004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3005 0 1 2 100 hg38.150200.bed.split3005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3006 0 1 2 100 hg38.150200.bed.split3006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3007 0 1 2 100 hg38.150200.bed.split3007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3008 0 1 2 100 hg38.150200.bed.split3008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3009 0 1 2 100 hg38.150200.bed.split3009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split301 0 1 2 100 hg38.150200.bed.split301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3010 0 1 2 100 hg38.150200.bed.split3010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3011 0 1 2 100 hg38.150200.bed.split3011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3012 0 1 2 100 hg38.150200.bed.split3012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3013 0 1 2 100 hg38.150200.bed.split3013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3014 0 1 2 100 hg38.150200.bed.split3014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3015 0 1 2 100 hg38.150200.bed.split3015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3016 0 1 2 100 hg38.150200.bed.split3016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3017 0 1 2 100 hg38.150200.bed.split3017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3018 0 1 2 100 hg38.150200.bed.split3018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3019 0 1 2 100 hg38.150200.bed.split3019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split302 0 1 2 100 hg38.150200.bed.split302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3020 0 1 2 100 hg38.150200.bed.split3020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3021 0 1 2 100 hg38.150200.bed.split3021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3022 0 1 2 100 hg38.150200.bed.split3022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3023 0 1 2 100 hg38.150200.bed.split3023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3024 0 1 2 100 hg38.150200.bed.split3024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3025 0 1 2 100 hg38.150200.bed.split3025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3026 0 1 2 100 hg38.150200.bed.split3026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3027 0 1 2 100 hg38.150200.bed.split3027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3028 0 1 2 100 hg38.150200.bed.split3028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3029 0 1 2 100 hg38.150200.bed.split3029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split303 0 1 2 100 hg38.150200.bed.split303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3030 0 1 2 100 hg38.150200.bed.split3030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3031 0 1 2 100 hg38.150200.bed.split3031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3032 0 1 2 100 hg38.150200.bed.split3032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3033 0 1 2 100 hg38.150200.bed.split3033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3034 0 1 2 100 hg38.150200.bed.split3034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3035 0 1 2 100 hg38.150200.bed.split3035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3036 0 1 2 100 hg38.150200.bed.split3036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3037 0 1 2 100 hg38.150200.bed.split3037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3038 0 1 2 100 hg38.150200.bed.split3038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3039 0 1 2 100 hg38.150200.bed.split3039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split304 0 1 2 100 hg38.150200.bed.split304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3040 0 1 2 100 hg38.150200.bed.split3040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3041 0 1 2 100 hg38.150200.bed.split3041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3042 0 1 2 100 hg38.150200.bed.split3042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3043 0 1 2 100 hg38.150200.bed.split3043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3044 0 1 2 100 hg38.150200.bed.split3044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3045 0 1 2 100 hg38.150200.bed.split3045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3046 0 1 2 100 hg38.150200.bed.split3046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3047 0 1 2 100 hg38.150200.bed.split3047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3048 0 1 2 100 hg38.150200.bed.split3048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3049 0 1 2 100 hg38.150200.bed.split3049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split305 0 1 2 100 hg38.150200.bed.split305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3050 0 1 2 100 hg38.150200.bed.split3050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3051 0 1 2 100 hg38.150200.bed.split3051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3052 0 1 2 100 hg38.150200.bed.split3052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3053 0 1 2 100 hg38.150200.bed.split3053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3054 0 1 2 100 hg38.150200.bed.split3054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3055 0 1 2 100 hg38.150200.bed.split3055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3056 0 1 2 100 hg38.150200.bed.split3056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3057 0 1 2 100 hg38.150200.bed.split3057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3058 0 1 2 100 hg38.150200.bed.split3058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3059 0 1 2 100 hg38.150200.bed.split3059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split306 0 1 2 100 hg38.150200.bed.split306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3060 0 1 2 100 hg38.150200.bed.split3060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3061 0 1 2 100 hg38.150200.bed.split3061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3062 0 1 2 100 hg38.150200.bed.split3062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3063 0 1 2 100 hg38.150200.bed.split3063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3064 0 1 2 100 hg38.150200.bed.split3064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3065 0 1 2 100 hg38.150200.bed.split3065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3066 0 1 2 100 hg38.150200.bed.split3066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3067 0 1 2 100 hg38.150200.bed.split3067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3068 0 1 2 100 hg38.150200.bed.split3068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3069 0 1 2 100 hg38.150200.bed.split3069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split307 0 1 2 100 hg38.150200.bed.split307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3070 0 1 2 100 hg38.150200.bed.split3070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3071 0 1 2 100 hg38.150200.bed.split3071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3072 0 1 2 100 hg38.150200.bed.split3072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3073 0 1 2 100 hg38.150200.bed.split3073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3074 0 1 2 100 hg38.150200.bed.split3074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3075 0 1 2 100 hg38.150200.bed.split3075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3076 0 1 2 100 hg38.150200.bed.split3076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3077 0 1 2 100 hg38.150200.bed.split3077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3078 0 1 2 100 hg38.150200.bed.split3078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3079 0 1 2 100 hg38.150200.bed.split3079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split308 0 1 2 100 hg38.150200.bed.split308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3080 0 1 2 100 hg38.150200.bed.split3080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3081 0 1 2 100 hg38.150200.bed.split3081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3082 0 1 2 100 hg38.150200.bed.split3082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3083 0 1 2 100 hg38.150200.bed.split3083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3084 0 1 2 100 hg38.150200.bed.split3084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3085 0 1 2 100 hg38.150200.bed.split3085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3086 0 1 2 100 hg38.150200.bed.split3086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3087 0 1 2 100 hg38.150200.bed.split3087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3088 0 1 2 100 hg38.150200.bed.split3088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3089 0 1 2 100 hg38.150200.bed.split3089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split309 0 1 2 100 hg38.150200.bed.split309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3090 0 1 2 100 hg38.150200.bed.split3090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3091 0 1 2 100 hg38.150200.bed.split3091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3092 0 1 2 100 hg38.150200.bed.split3092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3093 0 1 2 100 hg38.150200.bed.split3093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3094 0 1 2 100 hg38.150200.bed.split3094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3095 0 1 2 100 hg38.150200.bed.split3095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3096 0 1 2 100 hg38.150200.bed.split3096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3097 0 1 2 100 hg38.150200.bed.split3097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3098 0 1 2 100 hg38.150200.bed.split3098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3099 0 1 2 100 hg38.150200.bed.split3099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split31 0 1 2 100 hg38.150200.bed.split31.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split310 0 1 2 100 hg38.150200.bed.split310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3100 0 1 2 100 hg38.150200.bed.split3100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3101 0 1 2 100 hg38.150200.bed.split3101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3102 0 1 2 100 hg38.150200.bed.split3102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3103 0 1 2 100 hg38.150200.bed.split3103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3104 0 1 2 100 hg38.150200.bed.split3104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3105 0 1 2 100 hg38.150200.bed.split3105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3106 0 1 2 100 hg38.150200.bed.split3106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3107 0 1 2 100 hg38.150200.bed.split3107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3108 0 1 2 100 hg38.150200.bed.split3108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3109 0 1 2 100 hg38.150200.bed.split3109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split311 0 1 2 100 hg38.150200.bed.split311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3110 0 1 2 100 hg38.150200.bed.split3110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3111 0 1 2 100 hg38.150200.bed.split3111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3112 0 1 2 100 hg38.150200.bed.split3112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3113 0 1 2 100 hg38.150200.bed.split3113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3114 0 1 2 100 hg38.150200.bed.split3114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3115 0 1 2 100 hg38.150200.bed.split3115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3116 0 1 2 100 hg38.150200.bed.split3116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3117 0 1 2 100 hg38.150200.bed.split3117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3118 0 1 2 100 hg38.150200.bed.split3118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3119 0 1 2 100 hg38.150200.bed.split3119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split312 0 1 2 100 hg38.150200.bed.split312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3120 0 1 2 100 hg38.150200.bed.split3120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3121 0 1 2 100 hg38.150200.bed.split3121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3122 0 1 2 100 hg38.150200.bed.split3122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3123 0 1 2 100 hg38.150200.bed.split3123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3124 0 1 2 100 hg38.150200.bed.split3124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3125 0 1 2 100 hg38.150200.bed.split3125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3126 0 1 2 100 hg38.150200.bed.split3126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3127 0 1 2 100 hg38.150200.bed.split3127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3128 0 1 2 100 hg38.150200.bed.split3128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3129 0 1 2 100 hg38.150200.bed.split3129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split313 0 1 2 100 hg38.150200.bed.split313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3130 0 1 2 100 hg38.150200.bed.split3130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3131 0 1 2 100 hg38.150200.bed.split3131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3132 0 1 2 100 hg38.150200.bed.split3132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3133 0 1 2 100 hg38.150200.bed.split3133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3134 0 1 2 100 hg38.150200.bed.split3134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3135 0 1 2 100 hg38.150200.bed.split3135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3136 0 1 2 100 hg38.150200.bed.split3136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3137 0 1 2 100 hg38.150200.bed.split3137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3138 0 1 2 100 hg38.150200.bed.split3138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3139 0 1 2 100 hg38.150200.bed.split3139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split314 0 1 2 100 hg38.150200.bed.split314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3140 0 1 2 100 hg38.150200.bed.split3140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3141 0 1 2 100 hg38.150200.bed.split3141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3142 0 1 2 100 hg38.150200.bed.split3142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3143 0 1 2 100 hg38.150200.bed.split3143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3144 0 1 2 100 hg38.150200.bed.split3144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3145 0 1 2 100 hg38.150200.bed.split3145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3146 0 1 2 100 hg38.150200.bed.split3146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3147 0 1 2 100 hg38.150200.bed.split3147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3148 0 1 2 100 hg38.150200.bed.split3148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3149 0 1 2 100 hg38.150200.bed.split3149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split315 0 1 2 100 hg38.150200.bed.split315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3150 0 1 2 100 hg38.150200.bed.split3150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3151 0 1 2 100 hg38.150200.bed.split3151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3152 0 1 2 100 hg38.150200.bed.split3152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3153 0 1 2 100 hg38.150200.bed.split3153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3154 0 1 2 100 hg38.150200.bed.split3154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3155 0 1 2 100 hg38.150200.bed.split3155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3156 0 1 2 100 hg38.150200.bed.split3156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3157 0 1 2 100 hg38.150200.bed.split3157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3158 0 1 2 100 hg38.150200.bed.split3158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3159 0 1 2 100 hg38.150200.bed.split3159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split316 0 1 2 100 hg38.150200.bed.split316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3160 0 1 2 100 hg38.150200.bed.split3160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3161 0 1 2 100 hg38.150200.bed.split3161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3162 0 1 2 100 hg38.150200.bed.split3162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3163 0 1 2 100 hg38.150200.bed.split3163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3164 0 1 2 100 hg38.150200.bed.split3164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3165 0 1 2 100 hg38.150200.bed.split3165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3166 0 1 2 100 hg38.150200.bed.split3166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3167 0 1 2 100 hg38.150200.bed.split3167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3168 0 1 2 100 hg38.150200.bed.split3168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3169 0 1 2 100 hg38.150200.bed.split3169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split317 0 1 2 100 hg38.150200.bed.split317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3170 0 1 2 100 hg38.150200.bed.split3170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3171 0 1 2 100 hg38.150200.bed.split3171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3172 0 1 2 100 hg38.150200.bed.split3172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3173 0 1 2 100 hg38.150200.bed.split3173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3174 0 1 2 100 hg38.150200.bed.split3174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3175 0 1 2 100 hg38.150200.bed.split3175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3176 0 1 2 100 hg38.150200.bed.split3176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3177 0 1 2 100 hg38.150200.bed.split3177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3178 0 1 2 100 hg38.150200.bed.split3178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3179 0 1 2 100 hg38.150200.bed.split3179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split318 0 1 2 100 hg38.150200.bed.split318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3180 0 1 2 100 hg38.150200.bed.split3180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3181 0 1 2 100 hg38.150200.bed.split3181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3182 0 1 2 100 hg38.150200.bed.split3182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3183 0 1 2 100 hg38.150200.bed.split3183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3184 0 1 2 100 hg38.150200.bed.split3184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3185 0 1 2 100 hg38.150200.bed.split3185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3186 0 1 2 100 hg38.150200.bed.split3186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3187 0 1 2 100 hg38.150200.bed.split3187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3188 0 1 2 100 hg38.150200.bed.split3188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3189 0 1 2 100 hg38.150200.bed.split3189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split319 0 1 2 100 hg38.150200.bed.split319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3190 0 1 2 100 hg38.150200.bed.split3190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3191 0 1 2 100 hg38.150200.bed.split3191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3192 0 1 2 100 hg38.150200.bed.split3192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3193 0 1 2 100 hg38.150200.bed.split3193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3194 0 1 2 100 hg38.150200.bed.split3194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3195 0 1 2 100 hg38.150200.bed.split3195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3196 0 1 2 100 hg38.150200.bed.split3196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3197 0 1 2 100 hg38.150200.bed.split3197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3198 0 1 2 100 hg38.150200.bed.split3198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3199 0 1 2 100 hg38.150200.bed.split3199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split32 0 1 2 100 hg38.150200.bed.split32.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split320 0 1 2 100 hg38.150200.bed.split320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3200 0 1 2 100 hg38.150200.bed.split3200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3201 0 1 2 100 hg38.150200.bed.split3201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3202 0 1 2 100 hg38.150200.bed.split3202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3203 0 1 2 100 hg38.150200.bed.split3203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3204 0 1 2 100 hg38.150200.bed.split3204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3205 0 1 2 100 hg38.150200.bed.split3205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3206 0 1 2 100 hg38.150200.bed.split3206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3207 0 1 2 100 hg38.150200.bed.split3207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3208 0 1 2 100 hg38.150200.bed.split3208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3209 0 1 2 100 hg38.150200.bed.split3209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split321 0 1 2 100 hg38.150200.bed.split321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3210 0 1 2 100 hg38.150200.bed.split3210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3211 0 1 2 100 hg38.150200.bed.split3211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3212 0 1 2 100 hg38.150200.bed.split3212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3213 0 1 2 100 hg38.150200.bed.split3213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3214 0 1 2 100 hg38.150200.bed.split3214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3215 0 1 2 100 hg38.150200.bed.split3215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3216 0 1 2 100 hg38.150200.bed.split3216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3217 0 1 2 100 hg38.150200.bed.split3217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3218 0 1 2 100 hg38.150200.bed.split3218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3219 0 1 2 100 hg38.150200.bed.split3219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split322 0 1 2 100 hg38.150200.bed.split322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3220 0 1 2 100 hg38.150200.bed.split3220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3221 0 1 2 100 hg38.150200.bed.split3221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3222 0 1 2 100 hg38.150200.bed.split3222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3223 0 1 2 100 hg38.150200.bed.split3223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3224 0 1 2 100 hg38.150200.bed.split3224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3225 0 1 2 100 hg38.150200.bed.split3225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3226 0 1 2 100 hg38.150200.bed.split3226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3227 0 1 2 100 hg38.150200.bed.split3227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3228 0 1 2 100 hg38.150200.bed.split3228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3229 0 1 2 100 hg38.150200.bed.split3229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split323 0 1 2 100 hg38.150200.bed.split323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3230 0 1 2 100 hg38.150200.bed.split3230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3231 0 1 2 100 hg38.150200.bed.split3231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3232 0 1 2 100 hg38.150200.bed.split3232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3233 0 1 2 100 hg38.150200.bed.split3233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3234 0 1 2 100 hg38.150200.bed.split3234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3235 0 1 2 100 hg38.150200.bed.split3235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3236 0 1 2 100 hg38.150200.bed.split3236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3237 0 1 2 100 hg38.150200.bed.split3237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3238 0 1 2 100 hg38.150200.bed.split3238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3239 0 1 2 100 hg38.150200.bed.split3239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split324 0 1 2 100 hg38.150200.bed.split324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3240 0 1 2 100 hg38.150200.bed.split3240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3241 0 1 2 100 hg38.150200.bed.split3241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3242 0 1 2 100 hg38.150200.bed.split3242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3243 0 1 2 100 hg38.150200.bed.split3243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3244 0 1 2 100 hg38.150200.bed.split3244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3245 0 1 2 100 hg38.150200.bed.split3245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3246 0 1 2 100 hg38.150200.bed.split3246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3247 0 1 2 100 hg38.150200.bed.split3247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3248 0 1 2 100 hg38.150200.bed.split3248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3249 0 1 2 100 hg38.150200.bed.split3249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split325 0 1 2 100 hg38.150200.bed.split325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3250 0 1 2 100 hg38.150200.bed.split3250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3251 0 1 2 100 hg38.150200.bed.split3251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3252 0 1 2 100 hg38.150200.bed.split3252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3253 0 1 2 100 hg38.150200.bed.split3253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3254 0 1 2 100 hg38.150200.bed.split3254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3255 0 1 2 100 hg38.150200.bed.split3255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3256 0 1 2 100 hg38.150200.bed.split3256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3257 0 1 2 100 hg38.150200.bed.split3257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3258 0 1 2 100 hg38.150200.bed.split3258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3259 0 1 2 100 hg38.150200.bed.split3259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split326 0 1 2 100 hg38.150200.bed.split326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3260 0 1 2 100 hg38.150200.bed.split3260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3261 0 1 2 100 hg38.150200.bed.split3261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3262 0 1 2 100 hg38.150200.bed.split3262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3263 0 1 2 100 hg38.150200.bed.split3263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3264 0 1 2 100 hg38.150200.bed.split3264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3265 0 1 2 100 hg38.150200.bed.split3265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3266 0 1 2 100 hg38.150200.bed.split3266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3267 0 1 2 100 hg38.150200.bed.split3267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3268 0 1 2 100 hg38.150200.bed.split3268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3269 0 1 2 100 hg38.150200.bed.split3269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split327 0 1 2 100 hg38.150200.bed.split327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3270 0 1 2 100 hg38.150200.bed.split3270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3271 0 1 2 100 hg38.150200.bed.split3271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3272 0 1 2 100 hg38.150200.bed.split3272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3273 0 1 2 100 hg38.150200.bed.split3273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3274 0 1 2 100 hg38.150200.bed.split3274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3275 0 1 2 100 hg38.150200.bed.split3275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3276 0 1 2 100 hg38.150200.bed.split3276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3277 0 1 2 100 hg38.150200.bed.split3277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3278 0 1 2 100 hg38.150200.bed.split3278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3279 0 1 2 100 hg38.150200.bed.split3279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split328 0 1 2 100 hg38.150200.bed.split328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3280 0 1 2 100 hg38.150200.bed.split3280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3281 0 1 2 100 hg38.150200.bed.split3281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3282 0 1 2 100 hg38.150200.bed.split3282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3283 0 1 2 100 hg38.150200.bed.split3283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3284 0 1 2 100 hg38.150200.bed.split3284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3285 0 1 2 100 hg38.150200.bed.split3285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3286 0 1 2 100 hg38.150200.bed.split3286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3287 0 1 2 100 hg38.150200.bed.split3287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3288 0 1 2 100 hg38.150200.bed.split3288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3289 0 1 2 100 hg38.150200.bed.split3289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split329 0 1 2 100 hg38.150200.bed.split329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3290 0 1 2 100 hg38.150200.bed.split3290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3291 0 1 2 100 hg38.150200.bed.split3291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3292 0 1 2 100 hg38.150200.bed.split3292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3293 0 1 2 100 hg38.150200.bed.split3293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3294 0 1 2 100 hg38.150200.bed.split3294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3295 0 1 2 100 hg38.150200.bed.split3295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3296 0 1 2 100 hg38.150200.bed.split3296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3297 0 1 2 100 hg38.150200.bed.split3297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3298 0 1 2 100 hg38.150200.bed.split3298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3299 0 1 2 100 hg38.150200.bed.split3299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split33 0 1 2 100 hg38.150200.bed.split33.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split330 0 1 2 100 hg38.150200.bed.split330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3300 0 1 2 100 hg38.150200.bed.split3300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3301 0 1 2 100 hg38.150200.bed.split3301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3302 0 1 2 100 hg38.150200.bed.split3302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3303 0 1 2 100 hg38.150200.bed.split3303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3304 0 1 2 100 hg38.150200.bed.split3304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3305 0 1 2 100 hg38.150200.bed.split3305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3306 0 1 2 100 hg38.150200.bed.split3306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3307 0 1 2 100 hg38.150200.bed.split3307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3308 0 1 2 100 hg38.150200.bed.split3308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3309 0 1 2 100 hg38.150200.bed.split3309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split331 0 1 2 100 hg38.150200.bed.split331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3310 0 1 2 100 hg38.150200.bed.split3310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3311 0 1 2 100 hg38.150200.bed.split3311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3312 0 1 2 100 hg38.150200.bed.split3312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3313 0 1 2 100 hg38.150200.bed.split3313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3314 0 1 2 100 hg38.150200.bed.split3314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3315 0 1 2 100 hg38.150200.bed.split3315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3316 0 1 2 100 hg38.150200.bed.split3316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3317 0 1 2 100 hg38.150200.bed.split3317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3318 0 1 2 100 hg38.150200.bed.split3318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3319 0 1 2 100 hg38.150200.bed.split3319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split332 0 1 2 100 hg38.150200.bed.split332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3320 0 1 2 100 hg38.150200.bed.split3320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3321 0 1 2 100 hg38.150200.bed.split3321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3322 0 1 2 100 hg38.150200.bed.split3322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3323 0 1 2 100 hg38.150200.bed.split3323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3324 0 1 2 100 hg38.150200.bed.split3324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3325 0 1 2 100 hg38.150200.bed.split3325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3326 0 1 2 100 hg38.150200.bed.split3326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3327 0 1 2 100 hg38.150200.bed.split3327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3328 0 1 2 100 hg38.150200.bed.split3328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3329 0 1 2 100 hg38.150200.bed.split3329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split333 0 1 2 100 hg38.150200.bed.split333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3330 0 1 2 100 hg38.150200.bed.split3330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3331 0 1 2 100 hg38.150200.bed.split3331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3332 0 1 2 100 hg38.150200.bed.split3332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3333 0 1 2 100 hg38.150200.bed.split3333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3334 0 1 2 100 hg38.150200.bed.split3334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3335 0 1 2 100 hg38.150200.bed.split3335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3336 0 1 2 100 hg38.150200.bed.split3336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3337 0 1 2 100 hg38.150200.bed.split3337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3338 0 1 2 100 hg38.150200.bed.split3338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3339 0 1 2 100 hg38.150200.bed.split3339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split334 0 1 2 100 hg38.150200.bed.split334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3340 0 1 2 100 hg38.150200.bed.split3340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3341 0 1 2 100 hg38.150200.bed.split3341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3342 0 1 2 100 hg38.150200.bed.split3342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3343 0 1 2 100 hg38.150200.bed.split3343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3344 0 1 2 100 hg38.150200.bed.split3344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3345 0 1 2 100 hg38.150200.bed.split3345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3346 0 1 2 100 hg38.150200.bed.split3346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3347 0 1 2 100 hg38.150200.bed.split3347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3348 0 1 2 100 hg38.150200.bed.split3348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3349 0 1 2 100 hg38.150200.bed.split3349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split335 0 1 2 100 hg38.150200.bed.split335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3350 0 1 2 100 hg38.150200.bed.split3350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3351 0 1 2 100 hg38.150200.bed.split3351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3352 0 1 2 100 hg38.150200.bed.split3352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3353 0 1 2 100 hg38.150200.bed.split3353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3354 0 1 2 100 hg38.150200.bed.split3354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3355 0 1 2 100 hg38.150200.bed.split3355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3356 0 1 2 100 hg38.150200.bed.split3356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3357 0 1 2 100 hg38.150200.bed.split3357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3358 0 1 2 100 hg38.150200.bed.split3358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3359 0 1 2 100 hg38.150200.bed.split3359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split336 0 1 2 100 hg38.150200.bed.split336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3360 0 1 2 100 hg38.150200.bed.split3360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3361 0 1 2 100 hg38.150200.bed.split3361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3362 0 1 2 100 hg38.150200.bed.split3362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3363 0 1 2 100 hg38.150200.bed.split3363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3364 0 1 2 100 hg38.150200.bed.split3364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3365 0 1 2 100 hg38.150200.bed.split3365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3366 0 1 2 100 hg38.150200.bed.split3366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3367 0 1 2 100 hg38.150200.bed.split3367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3368 0 1 2 100 hg38.150200.bed.split3368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3369 0 1 2 100 hg38.150200.bed.split3369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split337 0 1 2 100 hg38.150200.bed.split337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3370 0 1 2 100 hg38.150200.bed.split3370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3371 0 1 2 100 hg38.150200.bed.split3371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3372 0 1 2 100 hg38.150200.bed.split3372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3373 0 1 2 100 hg38.150200.bed.split3373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3374 0 1 2 100 hg38.150200.bed.split3374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3375 0 1 2 100 hg38.150200.bed.split3375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3376 0 1 2 100 hg38.150200.bed.split3376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3377 0 1 2 100 hg38.150200.bed.split3377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3378 0 1 2 100 hg38.150200.bed.split3378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3379 0 1 2 100 hg38.150200.bed.split3379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split338 0 1 2 100 hg38.150200.bed.split338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3380 0 1 2 100 hg38.150200.bed.split3380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3381 0 1 2 100 hg38.150200.bed.split3381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3382 0 1 2 100 hg38.150200.bed.split3382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3383 0 1 2 100 hg38.150200.bed.split3383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3384 0 1 2 100 hg38.150200.bed.split3384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3385 0 1 2 100 hg38.150200.bed.split3385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3386 0 1 2 100 hg38.150200.bed.split3386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3387 0 1 2 100 hg38.150200.bed.split3387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3388 0 1 2 100 hg38.150200.bed.split3388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3389 0 1 2 100 hg38.150200.bed.split3389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split339 0 1 2 100 hg38.150200.bed.split339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3390 0 1 2 100 hg38.150200.bed.split3390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3391 0 1 2 100 hg38.150200.bed.split3391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3392 0 1 2 100 hg38.150200.bed.split3392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3393 0 1 2 100 hg38.150200.bed.split3393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3394 0 1 2 100 hg38.150200.bed.split3394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3395 0 1 2 100 hg38.150200.bed.split3395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3396 0 1 2 100 hg38.150200.bed.split3396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3397 0 1 2 100 hg38.150200.bed.split3397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3398 0 1 2 100 hg38.150200.bed.split3398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3399 0 1 2 100 hg38.150200.bed.split3399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split34 0 1 2 100 hg38.150200.bed.split34.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split340 0 1 2 100 hg38.150200.bed.split340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3400 0 1 2 100 hg38.150200.bed.split3400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3401 0 1 2 100 hg38.150200.bed.split3401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3402 0 1 2 100 hg38.150200.bed.split3402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3403 0 1 2 100 hg38.150200.bed.split3403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3404 0 1 2 100 hg38.150200.bed.split3404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3405 0 1 2 100 hg38.150200.bed.split3405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3406 0 1 2 100 hg38.150200.bed.split3406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3407 0 1 2 100 hg38.150200.bed.split3407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3408 0 1 2 100 hg38.150200.bed.split3408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3409 0 1 2 100 hg38.150200.bed.split3409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split341 0 1 2 100 hg38.150200.bed.split341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3410 0 1 2 100 hg38.150200.bed.split3410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3411 0 1 2 100 hg38.150200.bed.split3411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3412 0 1 2 100 hg38.150200.bed.split3412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3413 0 1 2 100 hg38.150200.bed.split3413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3414 0 1 2 100 hg38.150200.bed.split3414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3415 0 1 2 100 hg38.150200.bed.split3415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3416 0 1 2 100 hg38.150200.bed.split3416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3417 0 1 2 100 hg38.150200.bed.split3417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3418 0 1 2 100 hg38.150200.bed.split3418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3419 0 1 2 100 hg38.150200.bed.split3419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split342 0 1 2 100 hg38.150200.bed.split342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3420 0 1 2 100 hg38.150200.bed.split3420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3421 0 1 2 100 hg38.150200.bed.split3421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3422 0 1 2 100 hg38.150200.bed.split3422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3423 0 1 2 100 hg38.150200.bed.split3423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3424 0 1 2 100 hg38.150200.bed.split3424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3425 0 1 2 100 hg38.150200.bed.split3425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3426 0 1 2 100 hg38.150200.bed.split3426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3427 0 1 2 100 hg38.150200.bed.split3427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3428 0 1 2 100 hg38.150200.bed.split3428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3429 0 1 2 100 hg38.150200.bed.split3429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split343 0 1 2 100 hg38.150200.bed.split343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3430 0 1 2 100 hg38.150200.bed.split3430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3431 0 1 2 100 hg38.150200.bed.split3431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3432 0 1 2 100 hg38.150200.bed.split3432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3433 0 1 2 100 hg38.150200.bed.split3433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3434 0 1 2 100 hg38.150200.bed.split3434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3435 0 1 2 100 hg38.150200.bed.split3435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3436 0 1 2 100 hg38.150200.bed.split3436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3437 0 1 2 100 hg38.150200.bed.split3437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3438 0 1 2 100 hg38.150200.bed.split3438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3439 0 1 2 100 hg38.150200.bed.split3439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split344 0 1 2 100 hg38.150200.bed.split344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3440 0 1 2 100 hg38.150200.bed.split3440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3441 0 1 2 100 hg38.150200.bed.split3441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3442 0 1 2 100 hg38.150200.bed.split3442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3443 0 1 2 100 hg38.150200.bed.split3443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3444 0 1 2 100 hg38.150200.bed.split3444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3445 0 1 2 100 hg38.150200.bed.split3445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3446 0 1 2 100 hg38.150200.bed.split3446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3447 0 1 2 100 hg38.150200.bed.split3447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3448 0 1 2 100 hg38.150200.bed.split3448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3449 0 1 2 100 hg38.150200.bed.split3449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split345 0 1 2 100 hg38.150200.bed.split345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3450 0 1 2 100 hg38.150200.bed.split3450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3451 0 1 2 100 hg38.150200.bed.split3451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3452 0 1 2 100 hg38.150200.bed.split3452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3453 0 1 2 100 hg38.150200.bed.split3453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3454 0 1 2 100 hg38.150200.bed.split3454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3455 0 1 2 100 hg38.150200.bed.split3455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3456 0 1 2 100 hg38.150200.bed.split3456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3457 0 1 2 100 hg38.150200.bed.split3457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3458 0 1 2 100 hg38.150200.bed.split3458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3459 0 1 2 100 hg38.150200.bed.split3459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split346 0 1 2 100 hg38.150200.bed.split346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3460 0 1 2 100 hg38.150200.bed.split3460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3461 0 1 2 100 hg38.150200.bed.split3461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3462 0 1 2 100 hg38.150200.bed.split3462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3463 0 1 2 100 hg38.150200.bed.split3463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3464 0 1 2 100 hg38.150200.bed.split3464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3465 0 1 2 100 hg38.150200.bed.split3465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3466 0 1 2 100 hg38.150200.bed.split3466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3467 0 1 2 100 hg38.150200.bed.split3467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3468 0 1 2 100 hg38.150200.bed.split3468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3469 0 1 2 100 hg38.150200.bed.split3469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split347 0 1 2 100 hg38.150200.bed.split347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3470 0 1 2 100 hg38.150200.bed.split3470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3471 0 1 2 100 hg38.150200.bed.split3471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3472 0 1 2 100 hg38.150200.bed.split3472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3473 0 1 2 100 hg38.150200.bed.split3473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3474 0 1 2 100 hg38.150200.bed.split3474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3475 0 1 2 100 hg38.150200.bed.split3475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3476 0 1 2 100 hg38.150200.bed.split3476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3477 0 1 2 100 hg38.150200.bed.split3477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3478 0 1 2 100 hg38.150200.bed.split3478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3479 0 1 2 100 hg38.150200.bed.split3479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split348 0 1 2 100 hg38.150200.bed.split348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3480 0 1 2 100 hg38.150200.bed.split3480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3481 0 1 2 100 hg38.150200.bed.split3481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3482 0 1 2 100 hg38.150200.bed.split3482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3483 0 1 2 100 hg38.150200.bed.split3483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3484 0 1 2 100 hg38.150200.bed.split3484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3485 0 1 2 100 hg38.150200.bed.split3485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3486 0 1 2 100 hg38.150200.bed.split3486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3487 0 1 2 100 hg38.150200.bed.split3487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3488 0 1 2 100 hg38.150200.bed.split3488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3489 0 1 2 100 hg38.150200.bed.split3489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split349 0 1 2 100 hg38.150200.bed.split349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3490 0 1 2 100 hg38.150200.bed.split3490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3491 0 1 2 100 hg38.150200.bed.split3491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3492 0 1 2 100 hg38.150200.bed.split3492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3493 0 1 2 100 hg38.150200.bed.split3493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3494 0 1 2 100 hg38.150200.bed.split3494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3495 0 1 2 100 hg38.150200.bed.split3495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3496 0 1 2 100 hg38.150200.bed.split3496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3497 0 1 2 100 hg38.150200.bed.split3497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3498 0 1 2 100 hg38.150200.bed.split3498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3499 0 1 2 100 hg38.150200.bed.split3499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split35 0 1 2 100 hg38.150200.bed.split35.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split350 0 1 2 100 hg38.150200.bed.split350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3500 0 1 2 100 hg38.150200.bed.split3500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3501 0 1 2 100 hg38.150200.bed.split3501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3502 0 1 2 100 hg38.150200.bed.split3502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3503 0 1 2 100 hg38.150200.bed.split3503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3504 0 1 2 100 hg38.150200.bed.split3504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3505 0 1 2 100 hg38.150200.bed.split3505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3506 0 1 2 100 hg38.150200.bed.split3506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3507 0 1 2 100 hg38.150200.bed.split3507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3508 0 1 2 100 hg38.150200.bed.split3508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3509 0 1 2 100 hg38.150200.bed.split3509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split351 0 1 2 100 hg38.150200.bed.split351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3510 0 1 2 100 hg38.150200.bed.split3510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3511 0 1 2 100 hg38.150200.bed.split3511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3512 0 1 2 100 hg38.150200.bed.split3512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3513 0 1 2 100 hg38.150200.bed.split3513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3514 0 1 2 100 hg38.150200.bed.split3514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3515 0 1 2 100 hg38.150200.bed.split3515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3516 0 1 2 100 hg38.150200.bed.split3516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3517 0 1 2 100 hg38.150200.bed.split3517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3518 0 1 2 100 hg38.150200.bed.split3518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3519 0 1 2 100 hg38.150200.bed.split3519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split352 0 1 2 100 hg38.150200.bed.split352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3520 0 1 2 100 hg38.150200.bed.split3520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3521 0 1 2 100 hg38.150200.bed.split3521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3522 0 1 2 100 hg38.150200.bed.split3522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3523 0 1 2 100 hg38.150200.bed.split3523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3524 0 1 2 100 hg38.150200.bed.split3524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3525 0 1 2 100 hg38.150200.bed.split3525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3526 0 1 2 100 hg38.150200.bed.split3526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3527 0 1 2 100 hg38.150200.bed.split3527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3528 0 1 2 100 hg38.150200.bed.split3528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3529 0 1 2 100 hg38.150200.bed.split3529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split353 0 1 2 100 hg38.150200.bed.split353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3530 0 1 2 100 hg38.150200.bed.split3530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3531 0 1 2 100 hg38.150200.bed.split3531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3532 0 1 2 100 hg38.150200.bed.split3532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3533 0 1 2 100 hg38.150200.bed.split3533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3534 0 1 2 100 hg38.150200.bed.split3534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3535 0 1 2 100 hg38.150200.bed.split3535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3536 0 1 2 100 hg38.150200.bed.split3536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3537 0 1 2 100 hg38.150200.bed.split3537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3538 0 1 2 100 hg38.150200.bed.split3538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3539 0 1 2 100 hg38.150200.bed.split3539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split354 0 1 2 100 hg38.150200.bed.split354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3540 0 1 2 100 hg38.150200.bed.split3540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3541 0 1 2 100 hg38.150200.bed.split3541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3542 0 1 2 100 hg38.150200.bed.split3542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3543 0 1 2 100 hg38.150200.bed.split3543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3544 0 1 2 100 hg38.150200.bed.split3544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3545 0 1 2 100 hg38.150200.bed.split3545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3546 0 1 2 100 hg38.150200.bed.split3546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3547 0 1 2 100 hg38.150200.bed.split3547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3548 0 1 2 100 hg38.150200.bed.split3548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3549 0 1 2 100 hg38.150200.bed.split3549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split355 0 1 2 100 hg38.150200.bed.split355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3550 0 1 2 100 hg38.150200.bed.split3550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3551 0 1 2 100 hg38.150200.bed.split3551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3552 0 1 2 100 hg38.150200.bed.split3552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3553 0 1 2 100 hg38.150200.bed.split3553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3554 0 1 2 100 hg38.150200.bed.split3554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3555 0 1 2 100 hg38.150200.bed.split3555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3556 0 1 2 100 hg38.150200.bed.split3556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3557 0 1 2 100 hg38.150200.bed.split3557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3558 0 1 2 100 hg38.150200.bed.split3558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3559 0 1 2 100 hg38.150200.bed.split3559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split356 0 1 2 100 hg38.150200.bed.split356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3560 0 1 2 100 hg38.150200.bed.split3560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3561 0 1 2 100 hg38.150200.bed.split3561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3562 0 1 2 100 hg38.150200.bed.split3562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3563 0 1 2 100 hg38.150200.bed.split3563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3564 0 1 2 100 hg38.150200.bed.split3564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3565 0 1 2 100 hg38.150200.bed.split3565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3566 0 1 2 100 hg38.150200.bed.split3566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3567 0 1 2 100 hg38.150200.bed.split3567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3568 0 1 2 100 hg38.150200.bed.split3568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3569 0 1 2 100 hg38.150200.bed.split3569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split357 0 1 2 100 hg38.150200.bed.split357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3570 0 1 2 100 hg38.150200.bed.split3570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3571 0 1 2 100 hg38.150200.bed.split3571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3572 0 1 2 100 hg38.150200.bed.split3572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3573 0 1 2 100 hg38.150200.bed.split3573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3574 0 1 2 100 hg38.150200.bed.split3574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3575 0 1 2 100 hg38.150200.bed.split3575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3576 0 1 2 100 hg38.150200.bed.split3576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3577 0 1 2 100 hg38.150200.bed.split3577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3578 0 1 2 100 hg38.150200.bed.split3578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3579 0 1 2 100 hg38.150200.bed.split3579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split358 0 1 2 100 hg38.150200.bed.split358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3580 0 1 2 100 hg38.150200.bed.split3580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3581 0 1 2 100 hg38.150200.bed.split3581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3582 0 1 2 100 hg38.150200.bed.split3582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3583 0 1 2 100 hg38.150200.bed.split3583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3584 0 1 2 100 hg38.150200.bed.split3584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3585 0 1 2 100 hg38.150200.bed.split3585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3586 0 1 2 100 hg38.150200.bed.split3586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3587 0 1 2 100 hg38.150200.bed.split3587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3588 0 1 2 100 hg38.150200.bed.split3588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3589 0 1 2 100 hg38.150200.bed.split3589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split359 0 1 2 100 hg38.150200.bed.split359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3590 0 1 2 100 hg38.150200.bed.split3590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3591 0 1 2 100 hg38.150200.bed.split3591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3592 0 1 2 100 hg38.150200.bed.split3592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3593 0 1 2 100 hg38.150200.bed.split3593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3594 0 1 2 100 hg38.150200.bed.split3594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3595 0 1 2 100 hg38.150200.bed.split3595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3596 0 1 2 100 hg38.150200.bed.split3596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3597 0 1 2 100 hg38.150200.bed.split3597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3598 0 1 2 100 hg38.150200.bed.split3598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3599 0 1 2 100 hg38.150200.bed.split3599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split36 0 1 2 100 hg38.150200.bed.split36.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split360 0 1 2 100 hg38.150200.bed.split360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3600 0 1 2 100 hg38.150200.bed.split3600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3601 0 1 2 100 hg38.150200.bed.split3601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3602 0 1 2 100 hg38.150200.bed.split3602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3603 0 1 2 100 hg38.150200.bed.split3603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3604 0 1 2 100 hg38.150200.bed.split3604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3605 0 1 2 100 hg38.150200.bed.split3605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3606 0 1 2 100 hg38.150200.bed.split3606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3607 0 1 2 100 hg38.150200.bed.split3607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3608 0 1 2 100 hg38.150200.bed.split3608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3609 0 1 2 100 hg38.150200.bed.split3609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split361 0 1 2 100 hg38.150200.bed.split361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3610 0 1 2 100 hg38.150200.bed.split3610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3611 0 1 2 100 hg38.150200.bed.split3611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3612 0 1 2 100 hg38.150200.bed.split3612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3613 0 1 2 100 hg38.150200.bed.split3613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3614 0 1 2 100 hg38.150200.bed.split3614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3615 0 1 2 100 hg38.150200.bed.split3615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3616 0 1 2 100 hg38.150200.bed.split3616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3617 0 1 2 100 hg38.150200.bed.split3617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3618 0 1 2 100 hg38.150200.bed.split3618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3619 0 1 2 100 hg38.150200.bed.split3619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split362 0 1 2 100 hg38.150200.bed.split362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3620 0 1 2 100 hg38.150200.bed.split3620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3621 0 1 2 100 hg38.150200.bed.split3621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3622 0 1 2 100 hg38.150200.bed.split3622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3623 0 1 2 100 hg38.150200.bed.split3623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3624 0 1 2 100 hg38.150200.bed.split3624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3625 0 1 2 100 hg38.150200.bed.split3625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3626 0 1 2 100 hg38.150200.bed.split3626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3627 0 1 2 100 hg38.150200.bed.split3627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3628 0 1 2 100 hg38.150200.bed.split3628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3629 0 1 2 100 hg38.150200.bed.split3629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split363 0 1 2 100 hg38.150200.bed.split363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3630 0 1 2 100 hg38.150200.bed.split3630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3631 0 1 2 100 hg38.150200.bed.split3631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3632 0 1 2 100 hg38.150200.bed.split3632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3633 0 1 2 100 hg38.150200.bed.split3633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3634 0 1 2 100 hg38.150200.bed.split3634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3635 0 1 2 100 hg38.150200.bed.split3635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3636 0 1 2 100 hg38.150200.bed.split3636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3637 0 1 2 100 hg38.150200.bed.split3637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3638 0 1 2 100 hg38.150200.bed.split3638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3639 0 1 2 100 hg38.150200.bed.split3639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split364 0 1 2 100 hg38.150200.bed.split364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3640 0 1 2 100 hg38.150200.bed.split3640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3641 0 1 2 100 hg38.150200.bed.split3641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3642 0 1 2 100 hg38.150200.bed.split3642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3643 0 1 2 100 hg38.150200.bed.split3643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3644 0 1 2 100 hg38.150200.bed.split3644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3645 0 1 2 100 hg38.150200.bed.split3645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3646 0 1 2 100 hg38.150200.bed.split3646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3647 0 1 2 100 hg38.150200.bed.split3647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3648 0 1 2 100 hg38.150200.bed.split3648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3649 0 1 2 100 hg38.150200.bed.split3649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split365 0 1 2 100 hg38.150200.bed.split365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3650 0 1 2 100 hg38.150200.bed.split3650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3651 0 1 2 100 hg38.150200.bed.split3651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3652 0 1 2 100 hg38.150200.bed.split3652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3653 0 1 2 100 hg38.150200.bed.split3653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3654 0 1 2 100 hg38.150200.bed.split3654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3655 0 1 2 100 hg38.150200.bed.split3655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3656 0 1 2 100 hg38.150200.bed.split3656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3657 0 1 2 100 hg38.150200.bed.split3657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3658 0 1 2 100 hg38.150200.bed.split3658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3659 0 1 2 100 hg38.150200.bed.split3659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split366 0 1 2 100 hg38.150200.bed.split366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3660 0 1 2 100 hg38.150200.bed.split3660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3661 0 1 2 100 hg38.150200.bed.split3661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3662 0 1 2 100 hg38.150200.bed.split3662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3663 0 1 2 100 hg38.150200.bed.split3663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3664 0 1 2 100 hg38.150200.bed.split3664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3665 0 1 2 100 hg38.150200.bed.split3665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3666 0 1 2 100 hg38.150200.bed.split3666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3667 0 1 2 100 hg38.150200.bed.split3667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3668 0 1 2 100 hg38.150200.bed.split3668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3669 0 1 2 100 hg38.150200.bed.split3669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split367 0 1 2 100 hg38.150200.bed.split367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3670 0 1 2 100 hg38.150200.bed.split3670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3671 0 1 2 100 hg38.150200.bed.split3671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3672 0 1 2 100 hg38.150200.bed.split3672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3673 0 1 2 100 hg38.150200.bed.split3673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3674 0 1 2 100 hg38.150200.bed.split3674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3675 0 1 2 100 hg38.150200.bed.split3675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3676 0 1 2 100 hg38.150200.bed.split3676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3677 0 1 2 100 hg38.150200.bed.split3677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3678 0 1 2 100 hg38.150200.bed.split3678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3679 0 1 2 100 hg38.150200.bed.split3679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split368 0 1 2 100 hg38.150200.bed.split368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3680 0 1 2 100 hg38.150200.bed.split3680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3681 0 1 2 100 hg38.150200.bed.split3681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3682 0 1 2 100 hg38.150200.bed.split3682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3683 0 1 2 100 hg38.150200.bed.split3683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3684 0 1 2 100 hg38.150200.bed.split3684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3685 0 1 2 100 hg38.150200.bed.split3685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3686 0 1 2 100 hg38.150200.bed.split3686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3687 0 1 2 100 hg38.150200.bed.split3687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3688 0 1 2 100 hg38.150200.bed.split3688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3689 0 1 2 100 hg38.150200.bed.split3689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split369 0 1 2 100 hg38.150200.bed.split369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3690 0 1 2 100 hg38.150200.bed.split3690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3691 0 1 2 100 hg38.150200.bed.split3691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3692 0 1 2 100 hg38.150200.bed.split3692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3693 0 1 2 100 hg38.150200.bed.split3693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3694 0 1 2 100 hg38.150200.bed.split3694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3695 0 1 2 100 hg38.150200.bed.split3695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3696 0 1 2 100 hg38.150200.bed.split3696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3697 0 1 2 100 hg38.150200.bed.split3697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3698 0 1 2 100 hg38.150200.bed.split3698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3699 0 1 2 100 hg38.150200.bed.split3699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split37 0 1 2 100 hg38.150200.bed.split37.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split370 0 1 2 100 hg38.150200.bed.split370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3700 0 1 2 100 hg38.150200.bed.split3700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3701 0 1 2 100 hg38.150200.bed.split3701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3702 0 1 2 100 hg38.150200.bed.split3702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3703 0 1 2 100 hg38.150200.bed.split3703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3704 0 1 2 100 hg38.150200.bed.split3704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3705 0 1 2 100 hg38.150200.bed.split3705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3706 0 1 2 100 hg38.150200.bed.split3706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3707 0 1 2 100 hg38.150200.bed.split3707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3708 0 1 2 100 hg38.150200.bed.split3708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3709 0 1 2 100 hg38.150200.bed.split3709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split371 0 1 2 100 hg38.150200.bed.split371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3710 0 1 2 100 hg38.150200.bed.split3710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3711 0 1 2 100 hg38.150200.bed.split3711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3712 0 1 2 100 hg38.150200.bed.split3712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3713 0 1 2 100 hg38.150200.bed.split3713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3714 0 1 2 100 hg38.150200.bed.split3714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3715 0 1 2 100 hg38.150200.bed.split3715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3716 0 1 2 100 hg38.150200.bed.split3716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3717 0 1 2 100 hg38.150200.bed.split3717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3718 0 1 2 100 hg38.150200.bed.split3718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3719 0 1 2 100 hg38.150200.bed.split3719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split372 0 1 2 100 hg38.150200.bed.split372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3720 0 1 2 100 hg38.150200.bed.split3720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3721 0 1 2 100 hg38.150200.bed.split3721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3722 0 1 2 100 hg38.150200.bed.split3722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3723 0 1 2 100 hg38.150200.bed.split3723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3724 0 1 2 100 hg38.150200.bed.split3724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3725 0 1 2 100 hg38.150200.bed.split3725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3726 0 1 2 100 hg38.150200.bed.split3726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3727 0 1 2 100 hg38.150200.bed.split3727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3728 0 1 2 100 hg38.150200.bed.split3728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3729 0 1 2 100 hg38.150200.bed.split3729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split373 0 1 2 100 hg38.150200.bed.split373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3730 0 1 2 100 hg38.150200.bed.split3730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3731 0 1 2 100 hg38.150200.bed.split3731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3732 0 1 2 100 hg38.150200.bed.split3732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3733 0 1 2 100 hg38.150200.bed.split3733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3734 0 1 2 100 hg38.150200.bed.split3734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3735 0 1 2 100 hg38.150200.bed.split3735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3736 0 1 2 100 hg38.150200.bed.split3736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3737 0 1 2 100 hg38.150200.bed.split3737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3738 0 1 2 100 hg38.150200.bed.split3738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3739 0 1 2 100 hg38.150200.bed.split3739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split374 0 1 2 100 hg38.150200.bed.split374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3740 0 1 2 100 hg38.150200.bed.split3740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3741 0 1 2 100 hg38.150200.bed.split3741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3742 0 1 2 100 hg38.150200.bed.split3742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3743 0 1 2 100 hg38.150200.bed.split3743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3744 0 1 2 100 hg38.150200.bed.split3744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3745 0 1 2 100 hg38.150200.bed.split3745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3746 0 1 2 100 hg38.150200.bed.split3746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3747 0 1 2 100 hg38.150200.bed.split3747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3748 0 1 2 100 hg38.150200.bed.split3748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3749 0 1 2 100 hg38.150200.bed.split3749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split375 0 1 2 100 hg38.150200.bed.split375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3750 0 1 2 100 hg38.150200.bed.split3750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3751 0 1 2 100 hg38.150200.bed.split3751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3752 0 1 2 100 hg38.150200.bed.split3752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3753 0 1 2 100 hg38.150200.bed.split3753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3754 0 1 2 100 hg38.150200.bed.split3754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3755 0 1 2 100 hg38.150200.bed.split3755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3756 0 1 2 100 hg38.150200.bed.split3756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3757 0 1 2 100 hg38.150200.bed.split3757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3758 0 1 2 100 hg38.150200.bed.split3758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3759 0 1 2 100 hg38.150200.bed.split3759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split376 0 1 2 100 hg38.150200.bed.split376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3760 0 1 2 100 hg38.150200.bed.split3760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3761 0 1 2 100 hg38.150200.bed.split3761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3762 0 1 2 100 hg38.150200.bed.split3762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3763 0 1 2 100 hg38.150200.bed.split3763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3764 0 1 2 100 hg38.150200.bed.split3764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3765 0 1 2 100 hg38.150200.bed.split3765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3766 0 1 2 100 hg38.150200.bed.split3766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3767 0 1 2 100 hg38.150200.bed.split3767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3768 0 1 2 100 hg38.150200.bed.split3768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3769 0 1 2 100 hg38.150200.bed.split3769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split377 0 1 2 100 hg38.150200.bed.split377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3770 0 1 2 100 hg38.150200.bed.split3770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3771 0 1 2 100 hg38.150200.bed.split3771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3772 0 1 2 100 hg38.150200.bed.split3772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3773 0 1 2 100 hg38.150200.bed.split3773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3774 0 1 2 100 hg38.150200.bed.split3774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3775 0 1 2 100 hg38.150200.bed.split3775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3776 0 1 2 100 hg38.150200.bed.split3776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3777 0 1 2 100 hg38.150200.bed.split3777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3778 0 1 2 100 hg38.150200.bed.split3778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3779 0 1 2 100 hg38.150200.bed.split3779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split378 0 1 2 100 hg38.150200.bed.split378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3780 0 1 2 100 hg38.150200.bed.split3780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3781 0 1 2 100 hg38.150200.bed.split3781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3782 0 1 2 100 hg38.150200.bed.split3782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3783 0 1 2 100 hg38.150200.bed.split3783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3784 0 1 2 100 hg38.150200.bed.split3784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3785 0 1 2 100 hg38.150200.bed.split3785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3786 0 1 2 100 hg38.150200.bed.split3786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3787 0 1 2 100 hg38.150200.bed.split3787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3788 0 1 2 100 hg38.150200.bed.split3788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3789 0 1 2 100 hg38.150200.bed.split3789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split379 0 1 2 100 hg38.150200.bed.split379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3790 0 1 2 100 hg38.150200.bed.split3790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3791 0 1 2 100 hg38.150200.bed.split3791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3792 0 1 2 100 hg38.150200.bed.split3792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3793 0 1 2 100 hg38.150200.bed.split3793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3794 0 1 2 100 hg38.150200.bed.split3794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3795 0 1 2 100 hg38.150200.bed.split3795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3796 0 1 2 100 hg38.150200.bed.split3796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3797 0 1 2 100 hg38.150200.bed.split3797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3798 0 1 2 100 hg38.150200.bed.split3798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3799 0 1 2 100 hg38.150200.bed.split3799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split38 0 1 2 100 hg38.150200.bed.split38.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split380 0 1 2 100 hg38.150200.bed.split380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3800 0 1 2 100 hg38.150200.bed.split3800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3801 0 1 2 100 hg38.150200.bed.split3801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3802 0 1 2 100 hg38.150200.bed.split3802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3803 0 1 2 100 hg38.150200.bed.split3803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3804 0 1 2 100 hg38.150200.bed.split3804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3805 0 1 2 100 hg38.150200.bed.split3805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3806 0 1 2 100 hg38.150200.bed.split3806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3807 0 1 2 100 hg38.150200.bed.split3807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3808 0 1 2 100 hg38.150200.bed.split3808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3809 0 1 2 100 hg38.150200.bed.split3809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split381 0 1 2 100 hg38.150200.bed.split381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3810 0 1 2 100 hg38.150200.bed.split3810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3811 0 1 2 100 hg38.150200.bed.split3811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3812 0 1 2 100 hg38.150200.bed.split3812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3813 0 1 2 100 hg38.150200.bed.split3813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3814 0 1 2 100 hg38.150200.bed.split3814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3815 0 1 2 100 hg38.150200.bed.split3815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3816 0 1 2 100 hg38.150200.bed.split3816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3817 0 1 2 100 hg38.150200.bed.split3817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3818 0 1 2 100 hg38.150200.bed.split3818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3819 0 1 2 100 hg38.150200.bed.split3819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split382 0 1 2 100 hg38.150200.bed.split382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3820 0 1 2 100 hg38.150200.bed.split3820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3821 0 1 2 100 hg38.150200.bed.split3821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3822 0 1 2 100 hg38.150200.bed.split3822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3823 0 1 2 100 hg38.150200.bed.split3823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3824 0 1 2 100 hg38.150200.bed.split3824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3825 0 1 2 100 hg38.150200.bed.split3825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3826 0 1 2 100 hg38.150200.bed.split3826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3827 0 1 2 100 hg38.150200.bed.split3827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3828 0 1 2 100 hg38.150200.bed.split3828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3829 0 1 2 100 hg38.150200.bed.split3829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split383 0 1 2 100 hg38.150200.bed.split383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3830 0 1 2 100 hg38.150200.bed.split3830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3831 0 1 2 100 hg38.150200.bed.split3831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3832 0 1 2 100 hg38.150200.bed.split3832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3833 0 1 2 100 hg38.150200.bed.split3833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3834 0 1 2 100 hg38.150200.bed.split3834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3835 0 1 2 100 hg38.150200.bed.split3835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3836 0 1 2 100 hg38.150200.bed.split3836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3837 0 1 2 100 hg38.150200.bed.split3837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3838 0 1 2 100 hg38.150200.bed.split3838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3839 0 1 2 100 hg38.150200.bed.split3839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split384 0 1 2 100 hg38.150200.bed.split384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3840 0 1 2 100 hg38.150200.bed.split3840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3841 0 1 2 100 hg38.150200.bed.split3841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3842 0 1 2 100 hg38.150200.bed.split3842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3843 0 1 2 100 hg38.150200.bed.split3843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3844 0 1 2 100 hg38.150200.bed.split3844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3845 0 1 2 100 hg38.150200.bed.split3845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3846 0 1 2 100 hg38.150200.bed.split3846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3847 0 1 2 100 hg38.150200.bed.split3847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3848 0 1 2 100 hg38.150200.bed.split3848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3849 0 1 2 100 hg38.150200.bed.split3849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split385 0 1 2 100 hg38.150200.bed.split385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3850 0 1 2 100 hg38.150200.bed.split3850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3851 0 1 2 100 hg38.150200.bed.split3851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3852 0 1 2 100 hg38.150200.bed.split3852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3853 0 1 2 100 hg38.150200.bed.split3853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3854 0 1 2 100 hg38.150200.bed.split3854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3855 0 1 2 100 hg38.150200.bed.split3855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3856 0 1 2 100 hg38.150200.bed.split3856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3857 0 1 2 100 hg38.150200.bed.split3857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3858 0 1 2 100 hg38.150200.bed.split3858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3859 0 1 2 100 hg38.150200.bed.split3859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split386 0 1 2 100 hg38.150200.bed.split386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3860 0 1 2 100 hg38.150200.bed.split3860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3861 0 1 2 100 hg38.150200.bed.split3861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3862 0 1 2 100 hg38.150200.bed.split3862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3863 0 1 2 100 hg38.150200.bed.split3863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3864 0 1 2 100 hg38.150200.bed.split3864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3865 0 1 2 100 hg38.150200.bed.split3865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3866 0 1 2 100 hg38.150200.bed.split3866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3867 0 1 2 100 hg38.150200.bed.split3867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3868 0 1 2 100 hg38.150200.bed.split3868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3869 0 1 2 100 hg38.150200.bed.split3869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split387 0 1 2 100 hg38.150200.bed.split387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3870 0 1 2 100 hg38.150200.bed.split3870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3871 0 1 2 100 hg38.150200.bed.split3871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3872 0 1 2 100 hg38.150200.bed.split3872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3873 0 1 2 100 hg38.150200.bed.split3873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3874 0 1 2 100 hg38.150200.bed.split3874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3875 0 1 2 100 hg38.150200.bed.split3875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3876 0 1 2 100 hg38.150200.bed.split3876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3877 0 1 2 100 hg38.150200.bed.split3877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3878 0 1 2 100 hg38.150200.bed.split3878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3879 0 1 2 100 hg38.150200.bed.split3879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split388 0 1 2 100 hg38.150200.bed.split388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3880 0 1 2 100 hg38.150200.bed.split3880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3881 0 1 2 100 hg38.150200.bed.split3881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3882 0 1 2 100 hg38.150200.bed.split3882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3883 0 1 2 100 hg38.150200.bed.split3883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3884 0 1 2 100 hg38.150200.bed.split3884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3885 0 1 2 100 hg38.150200.bed.split3885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3886 0 1 2 100 hg38.150200.bed.split3886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3887 0 1 2 100 hg38.150200.bed.split3887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3888 0 1 2 100 hg38.150200.bed.split3888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3889 0 1 2 100 hg38.150200.bed.split3889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split389 0 1 2 100 hg38.150200.bed.split389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3890 0 1 2 100 hg38.150200.bed.split3890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3891 0 1 2 100 hg38.150200.bed.split3891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3892 0 1 2 100 hg38.150200.bed.split3892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3893 0 1 2 100 hg38.150200.bed.split3893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3894 0 1 2 100 hg38.150200.bed.split3894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3895 0 1 2 100 hg38.150200.bed.split3895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3896 0 1 2 100 hg38.150200.bed.split3896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3897 0 1 2 100 hg38.150200.bed.split3897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3898 0 1 2 100 hg38.150200.bed.split3898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3899 0 1 2 100 hg38.150200.bed.split3899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split39 0 1 2 100 hg38.150200.bed.split39.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split390 0 1 2 100 hg38.150200.bed.split390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3900 0 1 2 100 hg38.150200.bed.split3900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3901 0 1 2 100 hg38.150200.bed.split3901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3902 0 1 2 100 hg38.150200.bed.split3902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3903 0 1 2 100 hg38.150200.bed.split3903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3904 0 1 2 100 hg38.150200.bed.split3904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3905 0 1 2 100 hg38.150200.bed.split3905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3906 0 1 2 100 hg38.150200.bed.split3906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3907 0 1 2 100 hg38.150200.bed.split3907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3908 0 1 2 100 hg38.150200.bed.split3908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3909 0 1 2 100 hg38.150200.bed.split3909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split391 0 1 2 100 hg38.150200.bed.split391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3910 0 1 2 100 hg38.150200.bed.split3910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3911 0 1 2 100 hg38.150200.bed.split3911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3912 0 1 2 100 hg38.150200.bed.split3912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3913 0 1 2 100 hg38.150200.bed.split3913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3914 0 1 2 100 hg38.150200.bed.split3914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3915 0 1 2 100 hg38.150200.bed.split3915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3916 0 1 2 100 hg38.150200.bed.split3916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3917 0 1 2 100 hg38.150200.bed.split3917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3918 0 1 2 100 hg38.150200.bed.split3918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3919 0 1 2 100 hg38.150200.bed.split3919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split392 0 1 2 100 hg38.150200.bed.split392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3920 0 1 2 100 hg38.150200.bed.split3920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3921 0 1 2 100 hg38.150200.bed.split3921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3922 0 1 2 100 hg38.150200.bed.split3922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3923 0 1 2 100 hg38.150200.bed.split3923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3924 0 1 2 100 hg38.150200.bed.split3924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3925 0 1 2 100 hg38.150200.bed.split3925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3926 0 1 2 100 hg38.150200.bed.split3926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3927 0 1 2 100 hg38.150200.bed.split3927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3928 0 1 2 100 hg38.150200.bed.split3928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3929 0 1 2 100 hg38.150200.bed.split3929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split393 0 1 2 100 hg38.150200.bed.split393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3930 0 1 2 100 hg38.150200.bed.split3930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3931 0 1 2 100 hg38.150200.bed.split3931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3932 0 1 2 100 hg38.150200.bed.split3932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3933 0 1 2 100 hg38.150200.bed.split3933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3934 0 1 2 100 hg38.150200.bed.split3934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3935 0 1 2 100 hg38.150200.bed.split3935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3936 0 1 2 100 hg38.150200.bed.split3936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3937 0 1 2 100 hg38.150200.bed.split3937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3938 0 1 2 100 hg38.150200.bed.split3938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3939 0 1 2 100 hg38.150200.bed.split3939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split394 0 1 2 100 hg38.150200.bed.split394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3940 0 1 2 100 hg38.150200.bed.split3940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3941 0 1 2 100 hg38.150200.bed.split3941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3942 0 1 2 100 hg38.150200.bed.split3942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3943 0 1 2 100 hg38.150200.bed.split3943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3944 0 1 2 100 hg38.150200.bed.split3944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3945 0 1 2 100 hg38.150200.bed.split3945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3946 0 1 2 100 hg38.150200.bed.split3946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3947 0 1 2 100 hg38.150200.bed.split3947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3948 0 1 2 100 hg38.150200.bed.split3948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3949 0 1 2 100 hg38.150200.bed.split3949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split395 0 1 2 100 hg38.150200.bed.split395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3950 0 1 2 100 hg38.150200.bed.split3950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3951 0 1 2 100 hg38.150200.bed.split3951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3952 0 1 2 100 hg38.150200.bed.split3952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3953 0 1 2 100 hg38.150200.bed.split3953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3954 0 1 2 100 hg38.150200.bed.split3954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3955 0 1 2 100 hg38.150200.bed.split3955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3956 0 1 2 100 hg38.150200.bed.split3956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3957 0 1 2 100 hg38.150200.bed.split3957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3958 0 1 2 100 hg38.150200.bed.split3958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3959 0 1 2 100 hg38.150200.bed.split3959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split396 0 1 2 100 hg38.150200.bed.split396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3960 0 1 2 100 hg38.150200.bed.split3960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3961 0 1 2 100 hg38.150200.bed.split3961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3962 0 1 2 100 hg38.150200.bed.split3962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3963 0 1 2 100 hg38.150200.bed.split3963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3964 0 1 2 100 hg38.150200.bed.split3964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3965 0 1 2 100 hg38.150200.bed.split3965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3966 0 1 2 100 hg38.150200.bed.split3966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3967 0 1 2 100 hg38.150200.bed.split3967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3968 0 1 2 100 hg38.150200.bed.split3968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3969 0 1 2 100 hg38.150200.bed.split3969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split397 0 1 2 100 hg38.150200.bed.split397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3970 0 1 2 100 hg38.150200.bed.split3970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3971 0 1 2 100 hg38.150200.bed.split3971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3972 0 1 2 100 hg38.150200.bed.split3972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3973 0 1 2 100 hg38.150200.bed.split3973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3974 0 1 2 100 hg38.150200.bed.split3974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3975 0 1 2 100 hg38.150200.bed.split3975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3976 0 1 2 100 hg38.150200.bed.split3976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3977 0 1 2 100 hg38.150200.bed.split3977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3978 0 1 2 100 hg38.150200.bed.split3978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3979 0 1 2 100 hg38.150200.bed.split3979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split398 0 1 2 100 hg38.150200.bed.split398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3980 0 1 2 100 hg38.150200.bed.split3980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3981 0 1 2 100 hg38.150200.bed.split3981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3982 0 1 2 100 hg38.150200.bed.split3982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3983 0 1 2 100 hg38.150200.bed.split3983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3984 0 1 2 100 hg38.150200.bed.split3984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3985 0 1 2 100 hg38.150200.bed.split3985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3986 0 1 2 100 hg38.150200.bed.split3986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3987 0 1 2 100 hg38.150200.bed.split3987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3988 0 1 2 100 hg38.150200.bed.split3988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3989 0 1 2 100 hg38.150200.bed.split3989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split399 0 1 2 100 hg38.150200.bed.split399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3990 0 1 2 100 hg38.150200.bed.split3990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3991 0 1 2 100 hg38.150200.bed.split3991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3992 0 1 2 100 hg38.150200.bed.split3992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3993 0 1 2 100 hg38.150200.bed.split3993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3994 0 1 2 100 hg38.150200.bed.split3994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3995 0 1 2 100 hg38.150200.bed.split3995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3996 0 1 2 100 hg38.150200.bed.split3996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3997 0 1 2 100 hg38.150200.bed.split3997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3998 0 1 2 100 hg38.150200.bed.split3998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split3999 0 1 2 100 hg38.150200.bed.split3999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4 0 1 2 100 hg38.150200.bed.split4.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split40 0 1 2 100 hg38.150200.bed.split40.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split400 0 1 2 100 hg38.150200.bed.split400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4000 0 1 2 100 hg38.150200.bed.split4000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4001 0 1 2 100 hg38.150200.bed.split4001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4002 0 1 2 100 hg38.150200.bed.split4002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4003 0 1 2 100 hg38.150200.bed.split4003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4004 0 1 2 100 hg38.150200.bed.split4004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4005 0 1 2 100 hg38.150200.bed.split4005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4006 0 1 2 100 hg38.150200.bed.split4006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4007 0 1 2 100 hg38.150200.bed.split4007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4008 0 1 2 100 hg38.150200.bed.split4008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4009 0 1 2 100 hg38.150200.bed.split4009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split401 0 1 2 100 hg38.150200.bed.split401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4010 0 1 2 100 hg38.150200.bed.split4010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4011 0 1 2 100 hg38.150200.bed.split4011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4012 0 1 2 100 hg38.150200.bed.split4012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4013 0 1 2 100 hg38.150200.bed.split4013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4014 0 1 2 100 hg38.150200.bed.split4014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4015 0 1 2 100 hg38.150200.bed.split4015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4016 0 1 2 100 hg38.150200.bed.split4016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4017 0 1 2 100 hg38.150200.bed.split4017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4018 0 1 2 100 hg38.150200.bed.split4018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4019 0 1 2 100 hg38.150200.bed.split4019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split402 0 1 2 100 hg38.150200.bed.split402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4020 0 1 2 100 hg38.150200.bed.split4020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4021 0 1 2 100 hg38.150200.bed.split4021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4022 0 1 2 100 hg38.150200.bed.split4022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4023 0 1 2 100 hg38.150200.bed.split4023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4024 0 1 2 100 hg38.150200.bed.split4024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4025 0 1 2 100 hg38.150200.bed.split4025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4026 0 1 2 100 hg38.150200.bed.split4026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4027 0 1 2 100 hg38.150200.bed.split4027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4028 0 1 2 100 hg38.150200.bed.split4028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4029 0 1 2 100 hg38.150200.bed.split4029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split403 0 1 2 100 hg38.150200.bed.split403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4030 0 1 2 100 hg38.150200.bed.split4030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4031 0 1 2 100 hg38.150200.bed.split4031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4032 0 1 2 100 hg38.150200.bed.split4032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4033 0 1 2 100 hg38.150200.bed.split4033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4034 0 1 2 100 hg38.150200.bed.split4034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4035 0 1 2 100 hg38.150200.bed.split4035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4036 0 1 2 100 hg38.150200.bed.split4036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4037 0 1 2 100 hg38.150200.bed.split4037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4038 0 1 2 100 hg38.150200.bed.split4038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4039 0 1 2 100 hg38.150200.bed.split4039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split404 0 1 2 100 hg38.150200.bed.split404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4040 0 1 2 100 hg38.150200.bed.split4040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4041 0 1 2 100 hg38.150200.bed.split4041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4042 0 1 2 100 hg38.150200.bed.split4042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4043 0 1 2 100 hg38.150200.bed.split4043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4044 0 1 2 100 hg38.150200.bed.split4044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4045 0 1 2 100 hg38.150200.bed.split4045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4046 0 1 2 100 hg38.150200.bed.split4046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4047 0 1 2 100 hg38.150200.bed.split4047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4048 0 1 2 100 hg38.150200.bed.split4048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4049 0 1 2 100 hg38.150200.bed.split4049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split405 0 1 2 100 hg38.150200.bed.split405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4050 0 1 2 100 hg38.150200.bed.split4050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4051 0 1 2 100 hg38.150200.bed.split4051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4052 0 1 2 100 hg38.150200.bed.split4052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4053 0 1 2 100 hg38.150200.bed.split4053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4054 0 1 2 100 hg38.150200.bed.split4054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4055 0 1 2 100 hg38.150200.bed.split4055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4056 0 1 2 100 hg38.150200.bed.split4056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4057 0 1 2 100 hg38.150200.bed.split4057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4058 0 1 2 100 hg38.150200.bed.split4058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4059 0 1 2 100 hg38.150200.bed.split4059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split406 0 1 2 100 hg38.150200.bed.split406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4060 0 1 2 100 hg38.150200.bed.split4060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4061 0 1 2 100 hg38.150200.bed.split4061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4062 0 1 2 100 hg38.150200.bed.split4062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4063 0 1 2 100 hg38.150200.bed.split4063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4064 0 1 2 100 hg38.150200.bed.split4064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4065 0 1 2 100 hg38.150200.bed.split4065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4066 0 1 2 100 hg38.150200.bed.split4066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4067 0 1 2 100 hg38.150200.bed.split4067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4068 0 1 2 100 hg38.150200.bed.split4068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4069 0 1 2 100 hg38.150200.bed.split4069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split407 0 1 2 100 hg38.150200.bed.split407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4070 0 1 2 100 hg38.150200.bed.split4070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4071 0 1 2 100 hg38.150200.bed.split4071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4072 0 1 2 100 hg38.150200.bed.split4072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4073 0 1 2 100 hg38.150200.bed.split4073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4074 0 1 2 100 hg38.150200.bed.split4074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4075 0 1 2 100 hg38.150200.bed.split4075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4076 0 1 2 100 hg38.150200.bed.split4076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4077 0 1 2 100 hg38.150200.bed.split4077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4078 0 1 2 100 hg38.150200.bed.split4078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4079 0 1 2 100 hg38.150200.bed.split4079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split408 0 1 2 100 hg38.150200.bed.split408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4080 0 1 2 100 hg38.150200.bed.split4080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4081 0 1 2 100 hg38.150200.bed.split4081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4082 0 1 2 100 hg38.150200.bed.split4082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4083 0 1 2 100 hg38.150200.bed.split4083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4084 0 1 2 100 hg38.150200.bed.split4084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4085 0 1 2 100 hg38.150200.bed.split4085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4086 0 1 2 100 hg38.150200.bed.split4086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4087 0 1 2 100 hg38.150200.bed.split4087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4088 0 1 2 100 hg38.150200.bed.split4088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4089 0 1 2 100 hg38.150200.bed.split4089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split409 0 1 2 100 hg38.150200.bed.split409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4090 0 1 2 100 hg38.150200.bed.split4090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4091 0 1 2 100 hg38.150200.bed.split4091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4092 0 1 2 100 hg38.150200.bed.split4092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4093 0 1 2 100 hg38.150200.bed.split4093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4094 0 1 2 100 hg38.150200.bed.split4094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4095 0 1 2 100 hg38.150200.bed.split4095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4096 0 1 2 100 hg38.150200.bed.split4096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4097 0 1 2 100 hg38.150200.bed.split4097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4098 0 1 2 100 hg38.150200.bed.split4098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4099 0 1 2 100 hg38.150200.bed.split4099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split41 0 1 2 100 hg38.150200.bed.split41.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split410 0 1 2 100 hg38.150200.bed.split410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4100 0 1 2 100 hg38.150200.bed.split4100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4101 0 1 2 100 hg38.150200.bed.split4101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4102 0 1 2 100 hg38.150200.bed.split4102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4103 0 1 2 100 hg38.150200.bed.split4103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4104 0 1 2 100 hg38.150200.bed.split4104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4105 0 1 2 100 hg38.150200.bed.split4105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4106 0 1 2 100 hg38.150200.bed.split4106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4107 0 1 2 100 hg38.150200.bed.split4107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4108 0 1 2 100 hg38.150200.bed.split4108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4109 0 1 2 100 hg38.150200.bed.split4109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split411 0 1 2 100 hg38.150200.bed.split411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4110 0 1 2 100 hg38.150200.bed.split4110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4111 0 1 2 100 hg38.150200.bed.split4111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4112 0 1 2 100 hg38.150200.bed.split4112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4113 0 1 2 100 hg38.150200.bed.split4113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4114 0 1 2 100 hg38.150200.bed.split4114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4115 0 1 2 100 hg38.150200.bed.split4115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4116 0 1 2 100 hg38.150200.bed.split4116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4117 0 1 2 100 hg38.150200.bed.split4117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4118 0 1 2 100 hg38.150200.bed.split4118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4119 0 1 2 100 hg38.150200.bed.split4119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split412 0 1 2 100 hg38.150200.bed.split412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4120 0 1 2 100 hg38.150200.bed.split4120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4121 0 1 2 100 hg38.150200.bed.split4121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4122 0 1 2 100 hg38.150200.bed.split4122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4123 0 1 2 100 hg38.150200.bed.split4123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4124 0 1 2 100 hg38.150200.bed.split4124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4125 0 1 2 100 hg38.150200.bed.split4125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4126 0 1 2 100 hg38.150200.bed.split4126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4127 0 1 2 100 hg38.150200.bed.split4127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4128 0 1 2 100 hg38.150200.bed.split4128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4129 0 1 2 100 hg38.150200.bed.split4129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split413 0 1 2 100 hg38.150200.bed.split413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4130 0 1 2 100 hg38.150200.bed.split4130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4131 0 1 2 100 hg38.150200.bed.split4131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4132 0 1 2 100 hg38.150200.bed.split4132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4133 0 1 2 100 hg38.150200.bed.split4133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4134 0 1 2 100 hg38.150200.bed.split4134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4135 0 1 2 100 hg38.150200.bed.split4135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4136 0 1 2 100 hg38.150200.bed.split4136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4137 0 1 2 100 hg38.150200.bed.split4137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4138 0 1 2 100 hg38.150200.bed.split4138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4139 0 1 2 100 hg38.150200.bed.split4139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split414 0 1 2 100 hg38.150200.bed.split414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4140 0 1 2 100 hg38.150200.bed.split4140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4141 0 1 2 100 hg38.150200.bed.split4141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4142 0 1 2 100 hg38.150200.bed.split4142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4143 0 1 2 100 hg38.150200.bed.split4143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4144 0 1 2 100 hg38.150200.bed.split4144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4145 0 1 2 100 hg38.150200.bed.split4145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4146 0 1 2 100 hg38.150200.bed.split4146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4147 0 1 2 100 hg38.150200.bed.split4147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4148 0 1 2 100 hg38.150200.bed.split4148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4149 0 1 2 100 hg38.150200.bed.split4149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split415 0 1 2 100 hg38.150200.bed.split415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4150 0 1 2 100 hg38.150200.bed.split4150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4151 0 1 2 100 hg38.150200.bed.split4151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4152 0 1 2 100 hg38.150200.bed.split4152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4153 0 1 2 100 hg38.150200.bed.split4153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4154 0 1 2 100 hg38.150200.bed.split4154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4155 0 1 2 100 hg38.150200.bed.split4155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4156 0 1 2 100 hg38.150200.bed.split4156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4157 0 1 2 100 hg38.150200.bed.split4157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4158 0 1 2 100 hg38.150200.bed.split4158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4159 0 1 2 100 hg38.150200.bed.split4159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split416 0 1 2 100 hg38.150200.bed.split416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4160 0 1 2 100 hg38.150200.bed.split4160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4161 0 1 2 100 hg38.150200.bed.split4161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4162 0 1 2 100 hg38.150200.bed.split4162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4163 0 1 2 100 hg38.150200.bed.split4163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4164 0 1 2 100 hg38.150200.bed.split4164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4165 0 1 2 100 hg38.150200.bed.split4165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4166 0 1 2 100 hg38.150200.bed.split4166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4167 0 1 2 100 hg38.150200.bed.split4167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4168 0 1 2 100 hg38.150200.bed.split4168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4169 0 1 2 100 hg38.150200.bed.split4169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split417 0 1 2 100 hg38.150200.bed.split417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4170 0 1 2 100 hg38.150200.bed.split4170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4171 0 1 2 100 hg38.150200.bed.split4171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4172 0 1 2 100 hg38.150200.bed.split4172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4173 0 1 2 100 hg38.150200.bed.split4173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4174 0 1 2 100 hg38.150200.bed.split4174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4175 0 1 2 100 hg38.150200.bed.split4175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4176 0 1 2 100 hg38.150200.bed.split4176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4177 0 1 2 100 hg38.150200.bed.split4177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4178 0 1 2 100 hg38.150200.bed.split4178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4179 0 1 2 100 hg38.150200.bed.split4179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split418 0 1 2 100 hg38.150200.bed.split418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4180 0 1 2 100 hg38.150200.bed.split4180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4181 0 1 2 100 hg38.150200.bed.split4181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4182 0 1 2 100 hg38.150200.bed.split4182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4183 0 1 2 100 hg38.150200.bed.split4183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4184 0 1 2 100 hg38.150200.bed.split4184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4185 0 1 2 100 hg38.150200.bed.split4185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4186 0 1 2 100 hg38.150200.bed.split4186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4187 0 1 2 100 hg38.150200.bed.split4187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4188 0 1 2 100 hg38.150200.bed.split4188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4189 0 1 2 100 hg38.150200.bed.split4189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split419 0 1 2 100 hg38.150200.bed.split419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4190 0 1 2 100 hg38.150200.bed.split4190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4191 0 1 2 100 hg38.150200.bed.split4191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4192 0 1 2 100 hg38.150200.bed.split4192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4193 0 1 2 100 hg38.150200.bed.split4193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4194 0 1 2 100 hg38.150200.bed.split4194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4195 0 1 2 100 hg38.150200.bed.split4195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4196 0 1 2 100 hg38.150200.bed.split4196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4197 0 1 2 100 hg38.150200.bed.split4197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4198 0 1 2 100 hg38.150200.bed.split4198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4199 0 1 2 100 hg38.150200.bed.split4199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split42 0 1 2 100 hg38.150200.bed.split42.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split420 0 1 2 100 hg38.150200.bed.split420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4200 0 1 2 100 hg38.150200.bed.split4200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4201 0 1 2 100 hg38.150200.bed.split4201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4202 0 1 2 100 hg38.150200.bed.split4202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4203 0 1 2 100 hg38.150200.bed.split4203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4204 0 1 2 100 hg38.150200.bed.split4204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4205 0 1 2 100 hg38.150200.bed.split4205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4206 0 1 2 100 hg38.150200.bed.split4206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4207 0 1 2 100 hg38.150200.bed.split4207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4208 0 1 2 100 hg38.150200.bed.split4208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4209 0 1 2 100 hg38.150200.bed.split4209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split421 0 1 2 100 hg38.150200.bed.split421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4210 0 1 2 100 hg38.150200.bed.split4210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4211 0 1 2 100 hg38.150200.bed.split4211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4212 0 1 2 100 hg38.150200.bed.split4212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4213 0 1 2 100 hg38.150200.bed.split4213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4214 0 1 2 100 hg38.150200.bed.split4214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4215 0 1 2 100 hg38.150200.bed.split4215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4216 0 1 2 100 hg38.150200.bed.split4216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4217 0 1 2 100 hg38.150200.bed.split4217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4218 0 1 2 100 hg38.150200.bed.split4218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4219 0 1 2 100 hg38.150200.bed.split4219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split422 0 1 2 100 hg38.150200.bed.split422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4220 0 1 2 100 hg38.150200.bed.split4220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4221 0 1 2 100 hg38.150200.bed.split4221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4222 0 1 2 100 hg38.150200.bed.split4222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4223 0 1 2 100 hg38.150200.bed.split4223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4224 0 1 2 100 hg38.150200.bed.split4224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4225 0 1 2 100 hg38.150200.bed.split4225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4226 0 1 2 100 hg38.150200.bed.split4226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4227 0 1 2 100 hg38.150200.bed.split4227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4228 0 1 2 100 hg38.150200.bed.split4228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4229 0 1 2 100 hg38.150200.bed.split4229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split423 0 1 2 100 hg38.150200.bed.split423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4230 0 1 2 100 hg38.150200.bed.split4230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4231 0 1 2 100 hg38.150200.bed.split4231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4232 0 1 2 100 hg38.150200.bed.split4232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4233 0 1 2 100 hg38.150200.bed.split4233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4234 0 1 2 100 hg38.150200.bed.split4234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4235 0 1 2 100 hg38.150200.bed.split4235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4236 0 1 2 100 hg38.150200.bed.split4236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4237 0 1 2 100 hg38.150200.bed.split4237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4238 0 1 2 100 hg38.150200.bed.split4238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4239 0 1 2 100 hg38.150200.bed.split4239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split424 0 1 2 100 hg38.150200.bed.split424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4240 0 1 2 100 hg38.150200.bed.split4240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4241 0 1 2 100 hg38.150200.bed.split4241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4242 0 1 2 100 hg38.150200.bed.split4242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4243 0 1 2 100 hg38.150200.bed.split4243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4244 0 1 2 100 hg38.150200.bed.split4244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4245 0 1 2 100 hg38.150200.bed.split4245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4246 0 1 2 100 hg38.150200.bed.split4246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4247 0 1 2 100 hg38.150200.bed.split4247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4248 0 1 2 100 hg38.150200.bed.split4248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4249 0 1 2 100 hg38.150200.bed.split4249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split425 0 1 2 100 hg38.150200.bed.split425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4250 0 1 2 100 hg38.150200.bed.split4250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4251 0 1 2 100 hg38.150200.bed.split4251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4252 0 1 2 100 hg38.150200.bed.split4252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4253 0 1 2 100 hg38.150200.bed.split4253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4254 0 1 2 100 hg38.150200.bed.split4254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4255 0 1 2 100 hg38.150200.bed.split4255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4256 0 1 2 100 hg38.150200.bed.split4256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4257 0 1 2 100 hg38.150200.bed.split4257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4258 0 1 2 100 hg38.150200.bed.split4258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4259 0 1 2 100 hg38.150200.bed.split4259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split426 0 1 2 100 hg38.150200.bed.split426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4260 0 1 2 100 hg38.150200.bed.split4260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4261 0 1 2 100 hg38.150200.bed.split4261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4262 0 1 2 100 hg38.150200.bed.split4262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4263 0 1 2 100 hg38.150200.bed.split4263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4264 0 1 2 100 hg38.150200.bed.split4264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4265 0 1 2 100 hg38.150200.bed.split4265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4266 0 1 2 100 hg38.150200.bed.split4266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4267 0 1 2 100 hg38.150200.bed.split4267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4268 0 1 2 100 hg38.150200.bed.split4268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4269 0 1 2 100 hg38.150200.bed.split4269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split427 0 1 2 100 hg38.150200.bed.split427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4270 0 1 2 100 hg38.150200.bed.split4270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4271 0 1 2 100 hg38.150200.bed.split4271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4272 0 1 2 100 hg38.150200.bed.split4272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4273 0 1 2 100 hg38.150200.bed.split4273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4274 0 1 2 100 hg38.150200.bed.split4274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4275 0 1 2 100 hg38.150200.bed.split4275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4276 0 1 2 100 hg38.150200.bed.split4276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4277 0 1 2 100 hg38.150200.bed.split4277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4278 0 1 2 100 hg38.150200.bed.split4278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4279 0 1 2 100 hg38.150200.bed.split4279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split428 0 1 2 100 hg38.150200.bed.split428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4280 0 1 2 100 hg38.150200.bed.split4280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4281 0 1 2 100 hg38.150200.bed.split4281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4282 0 1 2 100 hg38.150200.bed.split4282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4283 0 1 2 100 hg38.150200.bed.split4283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4284 0 1 2 100 hg38.150200.bed.split4284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4285 0 1 2 100 hg38.150200.bed.split4285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4286 0 1 2 100 hg38.150200.bed.split4286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4287 0 1 2 100 hg38.150200.bed.split4287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4288 0 1 2 100 hg38.150200.bed.split4288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4289 0 1 2 100 hg38.150200.bed.split4289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split429 0 1 2 100 hg38.150200.bed.split429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4290 0 1 2 100 hg38.150200.bed.split4290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4291 0 1 2 100 hg38.150200.bed.split4291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4292 0 1 2 100 hg38.150200.bed.split4292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4293 0 1 2 100 hg38.150200.bed.split4293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4294 0 1 2 100 hg38.150200.bed.split4294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4295 0 1 2 100 hg38.150200.bed.split4295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4296 0 1 2 100 hg38.150200.bed.split4296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4297 0 1 2 100 hg38.150200.bed.split4297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4298 0 1 2 100 hg38.150200.bed.split4298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4299 0 1 2 100 hg38.150200.bed.split4299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split43 0 1 2 100 hg38.150200.bed.split43.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split430 0 1 2 100 hg38.150200.bed.split430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4300 0 1 2 100 hg38.150200.bed.split4300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4301 0 1 2 100 hg38.150200.bed.split4301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4302 0 1 2 100 hg38.150200.bed.split4302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4303 0 1 2 100 hg38.150200.bed.split4303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4304 0 1 2 100 hg38.150200.bed.split4304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4305 0 1 2 100 hg38.150200.bed.split4305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4306 0 1 2 100 hg38.150200.bed.split4306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4307 0 1 2 100 hg38.150200.bed.split4307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4308 0 1 2 100 hg38.150200.bed.split4308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4309 0 1 2 100 hg38.150200.bed.split4309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split431 0 1 2 100 hg38.150200.bed.split431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4310 0 1 2 100 hg38.150200.bed.split4310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4311 0 1 2 100 hg38.150200.bed.split4311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4312 0 1 2 100 hg38.150200.bed.split4312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4313 0 1 2 100 hg38.150200.bed.split4313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4314 0 1 2 100 hg38.150200.bed.split4314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4315 0 1 2 100 hg38.150200.bed.split4315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4316 0 1 2 100 hg38.150200.bed.split4316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4317 0 1 2 100 hg38.150200.bed.split4317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4318 0 1 2 100 hg38.150200.bed.split4318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4319 0 1 2 100 hg38.150200.bed.split4319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split432 0 1 2 100 hg38.150200.bed.split432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4320 0 1 2 100 hg38.150200.bed.split4320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4321 0 1 2 100 hg38.150200.bed.split4321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4322 0 1 2 100 hg38.150200.bed.split4322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4323 0 1 2 100 hg38.150200.bed.split4323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4324 0 1 2 100 hg38.150200.bed.split4324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4325 0 1 2 100 hg38.150200.bed.split4325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4326 0 1 2 100 hg38.150200.bed.split4326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4327 0 1 2 100 hg38.150200.bed.split4327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4328 0 1 2 100 hg38.150200.bed.split4328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4329 0 1 2 100 hg38.150200.bed.split4329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split433 0 1 2 100 hg38.150200.bed.split433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4330 0 1 2 100 hg38.150200.bed.split4330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4331 0 1 2 100 hg38.150200.bed.split4331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4332 0 1 2 100 hg38.150200.bed.split4332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4333 0 1 2 100 hg38.150200.bed.split4333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4334 0 1 2 100 hg38.150200.bed.split4334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4335 0 1 2 100 hg38.150200.bed.split4335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4336 0 1 2 100 hg38.150200.bed.split4336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4337 0 1 2 100 hg38.150200.bed.split4337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4338 0 1 2 100 hg38.150200.bed.split4338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4339 0 1 2 100 hg38.150200.bed.split4339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split434 0 1 2 100 hg38.150200.bed.split434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4340 0 1 2 100 hg38.150200.bed.split4340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4341 0 1 2 100 hg38.150200.bed.split4341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4342 0 1 2 100 hg38.150200.bed.split4342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4343 0 1 2 100 hg38.150200.bed.split4343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4344 0 1 2 100 hg38.150200.bed.split4344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4345 0 1 2 100 hg38.150200.bed.split4345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4346 0 1 2 100 hg38.150200.bed.split4346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4347 0 1 2 100 hg38.150200.bed.split4347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4348 0 1 2 100 hg38.150200.bed.split4348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4349 0 1 2 100 hg38.150200.bed.split4349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split435 0 1 2 100 hg38.150200.bed.split435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4350 0 1 2 100 hg38.150200.bed.split4350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4351 0 1 2 100 hg38.150200.bed.split4351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4352 0 1 2 100 hg38.150200.bed.split4352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4353 0 1 2 100 hg38.150200.bed.split4353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4354 0 1 2 100 hg38.150200.bed.split4354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4355 0 1 2 100 hg38.150200.bed.split4355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4356 0 1 2 100 hg38.150200.bed.split4356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4357 0 1 2 100 hg38.150200.bed.split4357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4358 0 1 2 100 hg38.150200.bed.split4358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4359 0 1 2 100 hg38.150200.bed.split4359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split436 0 1 2 100 hg38.150200.bed.split436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4360 0 1 2 100 hg38.150200.bed.split4360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4361 0 1 2 100 hg38.150200.bed.split4361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4362 0 1 2 100 hg38.150200.bed.split4362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4363 0 1 2 100 hg38.150200.bed.split4363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4364 0 1 2 100 hg38.150200.bed.split4364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4365 0 1 2 100 hg38.150200.bed.split4365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4366 0 1 2 100 hg38.150200.bed.split4366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4367 0 1 2 100 hg38.150200.bed.split4367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4368 0 1 2 100 hg38.150200.bed.split4368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4369 0 1 2 100 hg38.150200.bed.split4369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split437 0 1 2 100 hg38.150200.bed.split437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4370 0 1 2 100 hg38.150200.bed.split4370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4371 0 1 2 100 hg38.150200.bed.split4371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4372 0 1 2 100 hg38.150200.bed.split4372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4373 0 1 2 100 hg38.150200.bed.split4373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4374 0 1 2 100 hg38.150200.bed.split4374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4375 0 1 2 100 hg38.150200.bed.split4375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4376 0 1 2 100 hg38.150200.bed.split4376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4377 0 1 2 100 hg38.150200.bed.split4377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4378 0 1 2 100 hg38.150200.bed.split4378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4379 0 1 2 100 hg38.150200.bed.split4379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split438 0 1 2 100 hg38.150200.bed.split438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4380 0 1 2 100 hg38.150200.bed.split4380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4381 0 1 2 100 hg38.150200.bed.split4381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4382 0 1 2 100 hg38.150200.bed.split4382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4383 0 1 2 100 hg38.150200.bed.split4383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4384 0 1 2 100 hg38.150200.bed.split4384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4385 0 1 2 100 hg38.150200.bed.split4385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4386 0 1 2 100 hg38.150200.bed.split4386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4387 0 1 2 100 hg38.150200.bed.split4387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4388 0 1 2 100 hg38.150200.bed.split4388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4389 0 1 2 100 hg38.150200.bed.split4389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split439 0 1 2 100 hg38.150200.bed.split439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4390 0 1 2 100 hg38.150200.bed.split4390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4391 0 1 2 100 hg38.150200.bed.split4391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4392 0 1 2 100 hg38.150200.bed.split4392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4393 0 1 2 100 hg38.150200.bed.split4393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4394 0 1 2 100 hg38.150200.bed.split4394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4395 0 1 2 100 hg38.150200.bed.split4395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4396 0 1 2 100 hg38.150200.bed.split4396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4397 0 1 2 100 hg38.150200.bed.split4397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4398 0 1 2 100 hg38.150200.bed.split4398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4399 0 1 2 100 hg38.150200.bed.split4399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split44 0 1 2 100 hg38.150200.bed.split44.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split440 0 1 2 100 hg38.150200.bed.split440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4400 0 1 2 100 hg38.150200.bed.split4400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4401 0 1 2 100 hg38.150200.bed.split4401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4402 0 1 2 100 hg38.150200.bed.split4402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4403 0 1 2 100 hg38.150200.bed.split4403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4404 0 1 2 100 hg38.150200.bed.split4404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4405 0 1 2 100 hg38.150200.bed.split4405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4406 0 1 2 100 hg38.150200.bed.split4406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4407 0 1 2 100 hg38.150200.bed.split4407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4408 0 1 2 100 hg38.150200.bed.split4408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4409 0 1 2 100 hg38.150200.bed.split4409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split441 0 1 2 100 hg38.150200.bed.split441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4410 0 1 2 100 hg38.150200.bed.split4410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4411 0 1 2 100 hg38.150200.bed.split4411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4412 0 1 2 100 hg38.150200.bed.split4412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4413 0 1 2 100 hg38.150200.bed.split4413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4414 0 1 2 100 hg38.150200.bed.split4414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4415 0 1 2 100 hg38.150200.bed.split4415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4416 0 1 2 100 hg38.150200.bed.split4416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4417 0 1 2 100 hg38.150200.bed.split4417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4418 0 1 2 100 hg38.150200.bed.split4418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4419 0 1 2 100 hg38.150200.bed.split4419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split442 0 1 2 100 hg38.150200.bed.split442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4420 0 1 2 100 hg38.150200.bed.split4420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4421 0 1 2 100 hg38.150200.bed.split4421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4422 0 1 2 100 hg38.150200.bed.split4422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4423 0 1 2 100 hg38.150200.bed.split4423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4424 0 1 2 100 hg38.150200.bed.split4424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4425 0 1 2 100 hg38.150200.bed.split4425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4426 0 1 2 100 hg38.150200.bed.split4426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4427 0 1 2 100 hg38.150200.bed.split4427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4428 0 1 2 100 hg38.150200.bed.split4428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4429 0 1 2 100 hg38.150200.bed.split4429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split443 0 1 2 100 hg38.150200.bed.split443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4430 0 1 2 100 hg38.150200.bed.split4430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4431 0 1 2 100 hg38.150200.bed.split4431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4432 0 1 2 100 hg38.150200.bed.split4432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4433 0 1 2 100 hg38.150200.bed.split4433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4434 0 1 2 100 hg38.150200.bed.split4434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4435 0 1 2 100 hg38.150200.bed.split4435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4436 0 1 2 100 hg38.150200.bed.split4436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4437 0 1 2 100 hg38.150200.bed.split4437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4438 0 1 2 100 hg38.150200.bed.split4438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4439 0 1 2 100 hg38.150200.bed.split4439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split444 0 1 2 100 hg38.150200.bed.split444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4440 0 1 2 100 hg38.150200.bed.split4440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4441 0 1 2 100 hg38.150200.bed.split4441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4442 0 1 2 100 hg38.150200.bed.split4442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4443 0 1 2 100 hg38.150200.bed.split4443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4444 0 1 2 100 hg38.150200.bed.split4444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4445 0 1 2 100 hg38.150200.bed.split4445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4446 0 1 2 100 hg38.150200.bed.split4446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4447 0 1 2 100 hg38.150200.bed.split4447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4448 0 1 2 100 hg38.150200.bed.split4448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4449 0 1 2 100 hg38.150200.bed.split4449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split445 0 1 2 100 hg38.150200.bed.split445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4450 0 1 2 100 hg38.150200.bed.split4450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4451 0 1 2 100 hg38.150200.bed.split4451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4452 0 1 2 100 hg38.150200.bed.split4452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4453 0 1 2 100 hg38.150200.bed.split4453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4454 0 1 2 100 hg38.150200.bed.split4454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4455 0 1 2 100 hg38.150200.bed.split4455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4456 0 1 2 100 hg38.150200.bed.split4456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4457 0 1 2 100 hg38.150200.bed.split4457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4458 0 1 2 100 hg38.150200.bed.split4458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4459 0 1 2 100 hg38.150200.bed.split4459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split446 0 1 2 100 hg38.150200.bed.split446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4460 0 1 2 100 hg38.150200.bed.split4460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4461 0 1 2 100 hg38.150200.bed.split4461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4462 0 1 2 100 hg38.150200.bed.split4462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4463 0 1 2 100 hg38.150200.bed.split4463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4464 0 1 2 100 hg38.150200.bed.split4464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4465 0 1 2 100 hg38.150200.bed.split4465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4466 0 1 2 100 hg38.150200.bed.split4466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4467 0 1 2 100 hg38.150200.bed.split4467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4468 0 1 2 100 hg38.150200.bed.split4468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4469 0 1 2 100 hg38.150200.bed.split4469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split447 0 1 2 100 hg38.150200.bed.split447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4470 0 1 2 100 hg38.150200.bed.split4470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4471 0 1 2 100 hg38.150200.bed.split4471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4472 0 1 2 100 hg38.150200.bed.split4472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4473 0 1 2 100 hg38.150200.bed.split4473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4474 0 1 2 100 hg38.150200.bed.split4474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4475 0 1 2 100 hg38.150200.bed.split4475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4476 0 1 2 100 hg38.150200.bed.split4476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4477 0 1 2 100 hg38.150200.bed.split4477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4478 0 1 2 100 hg38.150200.bed.split4478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4479 0 1 2 100 hg38.150200.bed.split4479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split448 0 1 2 100 hg38.150200.bed.split448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4480 0 1 2 100 hg38.150200.bed.split4480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4481 0 1 2 100 hg38.150200.bed.split4481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4482 0 1 2 100 hg38.150200.bed.split4482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4483 0 1 2 100 hg38.150200.bed.split4483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4484 0 1 2 100 hg38.150200.bed.split4484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4485 0 1 2 100 hg38.150200.bed.split4485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4486 0 1 2 100 hg38.150200.bed.split4486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4487 0 1 2 100 hg38.150200.bed.split4487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4488 0 1 2 100 hg38.150200.bed.split4488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4489 0 1 2 100 hg38.150200.bed.split4489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split449 0 1 2 100 hg38.150200.bed.split449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4490 0 1 2 100 hg38.150200.bed.split4490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4491 0 1 2 100 hg38.150200.bed.split4491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4492 0 1 2 100 hg38.150200.bed.split4492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4493 0 1 2 100 hg38.150200.bed.split4493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4494 0 1 2 100 hg38.150200.bed.split4494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4495 0 1 2 100 hg38.150200.bed.split4495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4496 0 1 2 100 hg38.150200.bed.split4496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4497 0 1 2 100 hg38.150200.bed.split4497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4498 0 1 2 100 hg38.150200.bed.split4498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4499 0 1 2 100 hg38.150200.bed.split4499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split45 0 1 2 100 hg38.150200.bed.split45.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split450 0 1 2 100 hg38.150200.bed.split450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4500 0 1 2 100 hg38.150200.bed.split4500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4501 0 1 2 100 hg38.150200.bed.split4501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4502 0 1 2 100 hg38.150200.bed.split4502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4503 0 1 2 100 hg38.150200.bed.split4503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4504 0 1 2 100 hg38.150200.bed.split4504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4505 0 1 2 100 hg38.150200.bed.split4505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4506 0 1 2 100 hg38.150200.bed.split4506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4507 0 1 2 100 hg38.150200.bed.split4507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4508 0 1 2 100 hg38.150200.bed.split4508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4509 0 1 2 100 hg38.150200.bed.split4509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split451 0 1 2 100 hg38.150200.bed.split451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4510 0 1 2 100 hg38.150200.bed.split4510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4511 0 1 2 100 hg38.150200.bed.split4511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4512 0 1 2 100 hg38.150200.bed.split4512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4513 0 1 2 100 hg38.150200.bed.split4513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4514 0 1 2 100 hg38.150200.bed.split4514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4515 0 1 2 100 hg38.150200.bed.split4515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4516 0 1 2 100 hg38.150200.bed.split4516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4517 0 1 2 100 hg38.150200.bed.split4517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4518 0 1 2 100 hg38.150200.bed.split4518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4519 0 1 2 100 hg38.150200.bed.split4519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split452 0 1 2 100 hg38.150200.bed.split452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4520 0 1 2 100 hg38.150200.bed.split4520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4521 0 1 2 100 hg38.150200.bed.split4521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4522 0 1 2 100 hg38.150200.bed.split4522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4523 0 1 2 100 hg38.150200.bed.split4523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4524 0 1 2 100 hg38.150200.bed.split4524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4525 0 1 2 100 hg38.150200.bed.split4525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4526 0 1 2 100 hg38.150200.bed.split4526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4527 0 1 2 100 hg38.150200.bed.split4527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4528 0 1 2 100 hg38.150200.bed.split4528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4529 0 1 2 100 hg38.150200.bed.split4529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split453 0 1 2 100 hg38.150200.bed.split453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4530 0 1 2 100 hg38.150200.bed.split4530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4531 0 1 2 100 hg38.150200.bed.split4531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4532 0 1 2 100 hg38.150200.bed.split4532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4533 0 1 2 100 hg38.150200.bed.split4533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4534 0 1 2 100 hg38.150200.bed.split4534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4535 0 1 2 100 hg38.150200.bed.split4535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4536 0 1 2 100 hg38.150200.bed.split4536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4537 0 1 2 100 hg38.150200.bed.split4537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4538 0 1 2 100 hg38.150200.bed.split4538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4539 0 1 2 100 hg38.150200.bed.split4539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split454 0 1 2 100 hg38.150200.bed.split454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4540 0 1 2 100 hg38.150200.bed.split4540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4541 0 1 2 100 hg38.150200.bed.split4541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4542 0 1 2 100 hg38.150200.bed.split4542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4543 0 1 2 100 hg38.150200.bed.split4543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4544 0 1 2 100 hg38.150200.bed.split4544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4545 0 1 2 100 hg38.150200.bed.split4545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4546 0 1 2 100 hg38.150200.bed.split4546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4547 0 1 2 100 hg38.150200.bed.split4547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4548 0 1 2 100 hg38.150200.bed.split4548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4549 0 1 2 100 hg38.150200.bed.split4549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split455 0 1 2 100 hg38.150200.bed.split455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4550 0 1 2 100 hg38.150200.bed.split4550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4551 0 1 2 100 hg38.150200.bed.split4551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4552 0 1 2 100 hg38.150200.bed.split4552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4553 0 1 2 100 hg38.150200.bed.split4553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4554 0 1 2 100 hg38.150200.bed.split4554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4555 0 1 2 100 hg38.150200.bed.split4555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4556 0 1 2 100 hg38.150200.bed.split4556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4557 0 1 2 100 hg38.150200.bed.split4557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4558 0 1 2 100 hg38.150200.bed.split4558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4559 0 1 2 100 hg38.150200.bed.split4559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split456 0 1 2 100 hg38.150200.bed.split456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4560 0 1 2 100 hg38.150200.bed.split4560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4561 0 1 2 100 hg38.150200.bed.split4561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4562 0 1 2 100 hg38.150200.bed.split4562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4563 0 1 2 100 hg38.150200.bed.split4563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4564 0 1 2 100 hg38.150200.bed.split4564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4565 0 1 2 100 hg38.150200.bed.split4565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4566 0 1 2 100 hg38.150200.bed.split4566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4567 0 1 2 100 hg38.150200.bed.split4567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4568 0 1 2 100 hg38.150200.bed.split4568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4569 0 1 2 100 hg38.150200.bed.split4569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split457 0 1 2 100 hg38.150200.bed.split457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4570 0 1 2 100 hg38.150200.bed.split4570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4571 0 1 2 100 hg38.150200.bed.split4571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4572 0 1 2 100 hg38.150200.bed.split4572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4573 0 1 2 100 hg38.150200.bed.split4573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4574 0 1 2 100 hg38.150200.bed.split4574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4575 0 1 2 100 hg38.150200.bed.split4575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4576 0 1 2 100 hg38.150200.bed.split4576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4577 0 1 2 100 hg38.150200.bed.split4577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4578 0 1 2 100 hg38.150200.bed.split4578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4579 0 1 2 100 hg38.150200.bed.split4579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split458 0 1 2 100 hg38.150200.bed.split458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4580 0 1 2 100 hg38.150200.bed.split4580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4581 0 1 2 100 hg38.150200.bed.split4581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4582 0 1 2 100 hg38.150200.bed.split4582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4583 0 1 2 100 hg38.150200.bed.split4583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4584 0 1 2 100 hg38.150200.bed.split4584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4585 0 1 2 100 hg38.150200.bed.split4585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4586 0 1 2 100 hg38.150200.bed.split4586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4587 0 1 2 100 hg38.150200.bed.split4587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4588 0 1 2 100 hg38.150200.bed.split4588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4589 0 1 2 100 hg38.150200.bed.split4589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split459 0 1 2 100 hg38.150200.bed.split459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4590 0 1 2 100 hg38.150200.bed.split4590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4591 0 1 2 100 hg38.150200.bed.split4591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4592 0 1 2 100 hg38.150200.bed.split4592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4593 0 1 2 100 hg38.150200.bed.split4593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4594 0 1 2 100 hg38.150200.bed.split4594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4595 0 1 2 100 hg38.150200.bed.split4595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4596 0 1 2 100 hg38.150200.bed.split4596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4597 0 1 2 100 hg38.150200.bed.split4597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4598 0 1 2 100 hg38.150200.bed.split4598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4599 0 1 2 100 hg38.150200.bed.split4599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split46 0 1 2 100 hg38.150200.bed.split46.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split460 0 1 2 100 hg38.150200.bed.split460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4600 0 1 2 100 hg38.150200.bed.split4600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4601 0 1 2 100 hg38.150200.bed.split4601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4602 0 1 2 100 hg38.150200.bed.split4602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4603 0 1 2 100 hg38.150200.bed.split4603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4604 0 1 2 100 hg38.150200.bed.split4604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4605 0 1 2 100 hg38.150200.bed.split4605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4606 0 1 2 100 hg38.150200.bed.split4606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4607 0 1 2 100 hg38.150200.bed.split4607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4608 0 1 2 100 hg38.150200.bed.split4608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4609 0 1 2 100 hg38.150200.bed.split4609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split461 0 1 2 100 hg38.150200.bed.split461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4610 0 1 2 100 hg38.150200.bed.split4610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4611 0 1 2 100 hg38.150200.bed.split4611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4612 0 1 2 100 hg38.150200.bed.split4612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4613 0 1 2 100 hg38.150200.bed.split4613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4614 0 1 2 100 hg38.150200.bed.split4614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4615 0 1 2 100 hg38.150200.bed.split4615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4616 0 1 2 100 hg38.150200.bed.split4616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4617 0 1 2 100 hg38.150200.bed.split4617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4618 0 1 2 100 hg38.150200.bed.split4618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4619 0 1 2 100 hg38.150200.bed.split4619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split462 0 1 2 100 hg38.150200.bed.split462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4620 0 1 2 100 hg38.150200.bed.split4620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4621 0 1 2 100 hg38.150200.bed.split4621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4622 0 1 2 100 hg38.150200.bed.split4622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4623 0 1 2 100 hg38.150200.bed.split4623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4624 0 1 2 100 hg38.150200.bed.split4624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4625 0 1 2 100 hg38.150200.bed.split4625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4626 0 1 2 100 hg38.150200.bed.split4626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4627 0 1 2 100 hg38.150200.bed.split4627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4628 0 1 2 100 hg38.150200.bed.split4628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4629 0 1 2 100 hg38.150200.bed.split4629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split463 0 1 2 100 hg38.150200.bed.split463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4630 0 1 2 100 hg38.150200.bed.split4630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4631 0 1 2 100 hg38.150200.bed.split4631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4632 0 1 2 100 hg38.150200.bed.split4632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4633 0 1 2 100 hg38.150200.bed.split4633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4634 0 1 2 100 hg38.150200.bed.split4634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4635 0 1 2 100 hg38.150200.bed.split4635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4636 0 1 2 100 hg38.150200.bed.split4636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4637 0 1 2 100 hg38.150200.bed.split4637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4638 0 1 2 100 hg38.150200.bed.split4638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4639 0 1 2 100 hg38.150200.bed.split4639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split464 0 1 2 100 hg38.150200.bed.split464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4640 0 1 2 100 hg38.150200.bed.split4640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4641 0 1 2 100 hg38.150200.bed.split4641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4642 0 1 2 100 hg38.150200.bed.split4642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4643 0 1 2 100 hg38.150200.bed.split4643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4644 0 1 2 100 hg38.150200.bed.split4644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4645 0 1 2 100 hg38.150200.bed.split4645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4646 0 1 2 100 hg38.150200.bed.split4646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4647 0 1 2 100 hg38.150200.bed.split4647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4648 0 1 2 100 hg38.150200.bed.split4648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4649 0 1 2 100 hg38.150200.bed.split4649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split465 0 1 2 100 hg38.150200.bed.split465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4650 0 1 2 100 hg38.150200.bed.split4650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4651 0 1 2 100 hg38.150200.bed.split4651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4652 0 1 2 100 hg38.150200.bed.split4652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4653 0 1 2 100 hg38.150200.bed.split4653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4654 0 1 2 100 hg38.150200.bed.split4654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4655 0 1 2 100 hg38.150200.bed.split4655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4656 0 1 2 100 hg38.150200.bed.split4656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4657 0 1 2 100 hg38.150200.bed.split4657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4658 0 1 2 100 hg38.150200.bed.split4658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4659 0 1 2 100 hg38.150200.bed.split4659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split466 0 1 2 100 hg38.150200.bed.split466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4660 0 1 2 100 hg38.150200.bed.split4660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4661 0 1 2 100 hg38.150200.bed.split4661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4662 0 1 2 100 hg38.150200.bed.split4662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4663 0 1 2 100 hg38.150200.bed.split4663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4664 0 1 2 100 hg38.150200.bed.split4664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4665 0 1 2 100 hg38.150200.bed.split4665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4666 0 1 2 100 hg38.150200.bed.split4666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4667 0 1 2 100 hg38.150200.bed.split4667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4668 0 1 2 100 hg38.150200.bed.split4668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4669 0 1 2 100 hg38.150200.bed.split4669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split467 0 1 2 100 hg38.150200.bed.split467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4670 0 1 2 100 hg38.150200.bed.split4670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4671 0 1 2 100 hg38.150200.bed.split4671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4672 0 1 2 100 hg38.150200.bed.split4672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4673 0 1 2 100 hg38.150200.bed.split4673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4674 0 1 2 100 hg38.150200.bed.split4674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4675 0 1 2 100 hg38.150200.bed.split4675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4676 0 1 2 100 hg38.150200.bed.split4676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4677 0 1 2 100 hg38.150200.bed.split4677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4678 0 1 2 100 hg38.150200.bed.split4678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4679 0 1 2 100 hg38.150200.bed.split4679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split468 0 1 2 100 hg38.150200.bed.split468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4680 0 1 2 100 hg38.150200.bed.split4680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4681 0 1 2 100 hg38.150200.bed.split4681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4682 0 1 2 100 hg38.150200.bed.split4682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4683 0 1 2 100 hg38.150200.bed.split4683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4684 0 1 2 100 hg38.150200.bed.split4684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4685 0 1 2 100 hg38.150200.bed.split4685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4686 0 1 2 100 hg38.150200.bed.split4686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4687 0 1 2 100 hg38.150200.bed.split4687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4688 0 1 2 100 hg38.150200.bed.split4688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4689 0 1 2 100 hg38.150200.bed.split4689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split469 0 1 2 100 hg38.150200.bed.split469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4690 0 1 2 100 hg38.150200.bed.split4690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4691 0 1 2 100 hg38.150200.bed.split4691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4692 0 1 2 100 hg38.150200.bed.split4692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4693 0 1 2 100 hg38.150200.bed.split4693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4694 0 1 2 100 hg38.150200.bed.split4694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4695 0 1 2 100 hg38.150200.bed.split4695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4696 0 1 2 100 hg38.150200.bed.split4696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4697 0 1 2 100 hg38.150200.bed.split4697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4698 0 1 2 100 hg38.150200.bed.split4698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4699 0 1 2 100 hg38.150200.bed.split4699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split47 0 1 2 100 hg38.150200.bed.split47.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split470 0 1 2 100 hg38.150200.bed.split470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4700 0 1 2 100 hg38.150200.bed.split4700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4701 0 1 2 100 hg38.150200.bed.split4701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4702 0 1 2 100 hg38.150200.bed.split4702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4703 0 1 2 100 hg38.150200.bed.split4703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4704 0 1 2 100 hg38.150200.bed.split4704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4705 0 1 2 100 hg38.150200.bed.split4705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4706 0 1 2 100 hg38.150200.bed.split4706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4707 0 1 2 100 hg38.150200.bed.split4707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4708 0 1 2 100 hg38.150200.bed.split4708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4709 0 1 2 100 hg38.150200.bed.split4709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split471 0 1 2 100 hg38.150200.bed.split471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4710 0 1 2 100 hg38.150200.bed.split4710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4711 0 1 2 100 hg38.150200.bed.split4711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4712 0 1 2 100 hg38.150200.bed.split4712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4713 0 1 2 100 hg38.150200.bed.split4713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4714 0 1 2 100 hg38.150200.bed.split4714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4715 0 1 2 100 hg38.150200.bed.split4715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4716 0 1 2 100 hg38.150200.bed.split4716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4717 0 1 2 100 hg38.150200.bed.split4717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4718 0 1 2 100 hg38.150200.bed.split4718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4719 0 1 2 100 hg38.150200.bed.split4719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split472 0 1 2 100 hg38.150200.bed.split472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4720 0 1 2 100 hg38.150200.bed.split4720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4721 0 1 2 100 hg38.150200.bed.split4721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4722 0 1 2 100 hg38.150200.bed.split4722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4723 0 1 2 100 hg38.150200.bed.split4723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4724 0 1 2 100 hg38.150200.bed.split4724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4725 0 1 2 100 hg38.150200.bed.split4725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4726 0 1 2 100 hg38.150200.bed.split4726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4727 0 1 2 100 hg38.150200.bed.split4727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4728 0 1 2 100 hg38.150200.bed.split4728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4729 0 1 2 100 hg38.150200.bed.split4729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split473 0 1 2 100 hg38.150200.bed.split473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4730 0 1 2 100 hg38.150200.bed.split4730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4731 0 1 2 100 hg38.150200.bed.split4731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4732 0 1 2 100 hg38.150200.bed.split4732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4733 0 1 2 100 hg38.150200.bed.split4733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4734 0 1 2 100 hg38.150200.bed.split4734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4735 0 1 2 100 hg38.150200.bed.split4735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4736 0 1 2 100 hg38.150200.bed.split4736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4737 0 1 2 100 hg38.150200.bed.split4737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4738 0 1 2 100 hg38.150200.bed.split4738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4739 0 1 2 100 hg38.150200.bed.split4739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split474 0 1 2 100 hg38.150200.bed.split474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4740 0 1 2 100 hg38.150200.bed.split4740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4741 0 1 2 100 hg38.150200.bed.split4741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4742 0 1 2 100 hg38.150200.bed.split4742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4743 0 1 2 100 hg38.150200.bed.split4743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4744 0 1 2 100 hg38.150200.bed.split4744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4745 0 1 2 100 hg38.150200.bed.split4745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4746 0 1 2 100 hg38.150200.bed.split4746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4747 0 1 2 100 hg38.150200.bed.split4747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4748 0 1 2 100 hg38.150200.bed.split4748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4749 0 1 2 100 hg38.150200.bed.split4749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split475 0 1 2 100 hg38.150200.bed.split475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4750 0 1 2 100 hg38.150200.bed.split4750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4751 0 1 2 100 hg38.150200.bed.split4751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4752 0 1 2 100 hg38.150200.bed.split4752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4753 0 1 2 100 hg38.150200.bed.split4753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4754 0 1 2 100 hg38.150200.bed.split4754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4755 0 1 2 100 hg38.150200.bed.split4755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4756 0 1 2 100 hg38.150200.bed.split4756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4757 0 1 2 100 hg38.150200.bed.split4757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4758 0 1 2 100 hg38.150200.bed.split4758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4759 0 1 2 100 hg38.150200.bed.split4759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split476 0 1 2 100 hg38.150200.bed.split476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4760 0 1 2 100 hg38.150200.bed.split4760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4761 0 1 2 100 hg38.150200.bed.split4761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4762 0 1 2 100 hg38.150200.bed.split4762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4763 0 1 2 100 hg38.150200.bed.split4763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4764 0 1 2 100 hg38.150200.bed.split4764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4765 0 1 2 100 hg38.150200.bed.split4765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4766 0 1 2 100 hg38.150200.bed.split4766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4767 0 1 2 100 hg38.150200.bed.split4767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4768 0 1 2 100 hg38.150200.bed.split4768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4769 0 1 2 100 hg38.150200.bed.split4769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split477 0 1 2 100 hg38.150200.bed.split477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4770 0 1 2 100 hg38.150200.bed.split4770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4771 0 1 2 100 hg38.150200.bed.split4771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4772 0 1 2 100 hg38.150200.bed.split4772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4773 0 1 2 100 hg38.150200.bed.split4773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4774 0 1 2 100 hg38.150200.bed.split4774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4775 0 1 2 100 hg38.150200.bed.split4775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4776 0 1 2 100 hg38.150200.bed.split4776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4777 0 1 2 100 hg38.150200.bed.split4777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4778 0 1 2 100 hg38.150200.bed.split4778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4779 0 1 2 100 hg38.150200.bed.split4779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split478 0 1 2 100 hg38.150200.bed.split478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4780 0 1 2 100 hg38.150200.bed.split4780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4781 0 1 2 100 hg38.150200.bed.split4781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4782 0 1 2 100 hg38.150200.bed.split4782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4783 0 1 2 100 hg38.150200.bed.split4783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4784 0 1 2 100 hg38.150200.bed.split4784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4785 0 1 2 100 hg38.150200.bed.split4785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4786 0 1 2 100 hg38.150200.bed.split4786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4787 0 1 2 100 hg38.150200.bed.split4787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4788 0 1 2 100 hg38.150200.bed.split4788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4789 0 1 2 100 hg38.150200.bed.split4789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split479 0 1 2 100 hg38.150200.bed.split479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4790 0 1 2 100 hg38.150200.bed.split4790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4791 0 1 2 100 hg38.150200.bed.split4791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4792 0 1 2 100 hg38.150200.bed.split4792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4793 0 1 2 100 hg38.150200.bed.split4793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4794 0 1 2 100 hg38.150200.bed.split4794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4795 0 1 2 100 hg38.150200.bed.split4795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4796 0 1 2 100 hg38.150200.bed.split4796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4797 0 1 2 100 hg38.150200.bed.split4797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4798 0 1 2 100 hg38.150200.bed.split4798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4799 0 1 2 100 hg38.150200.bed.split4799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split48 0 1 2 100 hg38.150200.bed.split48.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split480 0 1 2 100 hg38.150200.bed.split480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4800 0 1 2 100 hg38.150200.bed.split4800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4801 0 1 2 100 hg38.150200.bed.split4801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4802 0 1 2 100 hg38.150200.bed.split4802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4803 0 1 2 100 hg38.150200.bed.split4803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4804 0 1 2 100 hg38.150200.bed.split4804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4805 0 1 2 100 hg38.150200.bed.split4805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4806 0 1 2 100 hg38.150200.bed.split4806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4807 0 1 2 100 hg38.150200.bed.split4807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4808 0 1 2 100 hg38.150200.bed.split4808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4809 0 1 2 100 hg38.150200.bed.split4809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split481 0 1 2 100 hg38.150200.bed.split481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4810 0 1 2 100 hg38.150200.bed.split4810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4811 0 1 2 100 hg38.150200.bed.split4811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4812 0 1 2 100 hg38.150200.bed.split4812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4813 0 1 2 100 hg38.150200.bed.split4813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4814 0 1 2 100 hg38.150200.bed.split4814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4815 0 1 2 100 hg38.150200.bed.split4815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4816 0 1 2 100 hg38.150200.bed.split4816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4817 0 1 2 100 hg38.150200.bed.split4817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4818 0 1 2 100 hg38.150200.bed.split4818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4819 0 1 2 100 hg38.150200.bed.split4819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split482 0 1 2 100 hg38.150200.bed.split482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4820 0 1 2 100 hg38.150200.bed.split4820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4821 0 1 2 100 hg38.150200.bed.split4821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4822 0 1 2 100 hg38.150200.bed.split4822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4823 0 1 2 100 hg38.150200.bed.split4823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4824 0 1 2 100 hg38.150200.bed.split4824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4825 0 1 2 100 hg38.150200.bed.split4825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4826 0 1 2 100 hg38.150200.bed.split4826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4827 0 1 2 100 hg38.150200.bed.split4827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4828 0 1 2 100 hg38.150200.bed.split4828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4829 0 1 2 100 hg38.150200.bed.split4829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split483 0 1 2 100 hg38.150200.bed.split483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4830 0 1 2 100 hg38.150200.bed.split4830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4831 0 1 2 100 hg38.150200.bed.split4831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4832 0 1 2 100 hg38.150200.bed.split4832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4833 0 1 2 100 hg38.150200.bed.split4833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4834 0 1 2 100 hg38.150200.bed.split4834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4835 0 1 2 100 hg38.150200.bed.split4835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4836 0 1 2 100 hg38.150200.bed.split4836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4837 0 1 2 100 hg38.150200.bed.split4837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4838 0 1 2 100 hg38.150200.bed.split4838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4839 0 1 2 100 hg38.150200.bed.split4839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split484 0 1 2 100 hg38.150200.bed.split484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4840 0 1 2 100 hg38.150200.bed.split4840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4841 0 1 2 100 hg38.150200.bed.split4841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4842 0 1 2 100 hg38.150200.bed.split4842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4843 0 1 2 100 hg38.150200.bed.split4843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4844 0 1 2 100 hg38.150200.bed.split4844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4845 0 1 2 100 hg38.150200.bed.split4845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4846 0 1 2 100 hg38.150200.bed.split4846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4847 0 1 2 100 hg38.150200.bed.split4847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4848 0 1 2 100 hg38.150200.bed.split4848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4849 0 1 2 100 hg38.150200.bed.split4849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split485 0 1 2 100 hg38.150200.bed.split485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4850 0 1 2 100 hg38.150200.bed.split4850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4851 0 1 2 100 hg38.150200.bed.split4851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4852 0 1 2 100 hg38.150200.bed.split4852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4853 0 1 2 100 hg38.150200.bed.split4853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4854 0 1 2 100 hg38.150200.bed.split4854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4855 0 1 2 100 hg38.150200.bed.split4855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4856 0 1 2 100 hg38.150200.bed.split4856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4857 0 1 2 100 hg38.150200.bed.split4857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4858 0 1 2 100 hg38.150200.bed.split4858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4859 0 1 2 100 hg38.150200.bed.split4859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split486 0 1 2 100 hg38.150200.bed.split486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4860 0 1 2 100 hg38.150200.bed.split4860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4861 0 1 2 100 hg38.150200.bed.split4861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4862 0 1 2 100 hg38.150200.bed.split4862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4863 0 1 2 100 hg38.150200.bed.split4863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4864 0 1 2 100 hg38.150200.bed.split4864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4865 0 1 2 100 hg38.150200.bed.split4865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4866 0 1 2 100 hg38.150200.bed.split4866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4867 0 1 2 100 hg38.150200.bed.split4867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4868 0 1 2 100 hg38.150200.bed.split4868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4869 0 1 2 100 hg38.150200.bed.split4869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split487 0 1 2 100 hg38.150200.bed.split487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4870 0 1 2 100 hg38.150200.bed.split4870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4871 0 1 2 100 hg38.150200.bed.split4871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4872 0 1 2 100 hg38.150200.bed.split4872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4873 0 1 2 100 hg38.150200.bed.split4873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4874 0 1 2 100 hg38.150200.bed.split4874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4875 0 1 2 100 hg38.150200.bed.split4875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4876 0 1 2 100 hg38.150200.bed.split4876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4877 0 1 2 100 hg38.150200.bed.split4877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4878 0 1 2 100 hg38.150200.bed.split4878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4879 0 1 2 100 hg38.150200.bed.split4879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split488 0 1 2 100 hg38.150200.bed.split488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4880 0 1 2 100 hg38.150200.bed.split4880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4881 0 1 2 100 hg38.150200.bed.split4881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4882 0 1 2 100 hg38.150200.bed.split4882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4883 0 1 2 100 hg38.150200.bed.split4883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4884 0 1 2 100 hg38.150200.bed.split4884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4885 0 1 2 100 hg38.150200.bed.split4885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4886 0 1 2 100 hg38.150200.bed.split4886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4887 0 1 2 100 hg38.150200.bed.split4887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4888 0 1 2 100 hg38.150200.bed.split4888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4889 0 1 2 100 hg38.150200.bed.split4889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split489 0 1 2 100 hg38.150200.bed.split489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4890 0 1 2 100 hg38.150200.bed.split4890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4891 0 1 2 100 hg38.150200.bed.split4891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4892 0 1 2 100 hg38.150200.bed.split4892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4893 0 1 2 100 hg38.150200.bed.split4893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4894 0 1 2 100 hg38.150200.bed.split4894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4895 0 1 2 100 hg38.150200.bed.split4895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4896 0 1 2 100 hg38.150200.bed.split4896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4897 0 1 2 100 hg38.150200.bed.split4897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4898 0 1 2 100 hg38.150200.bed.split4898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4899 0 1 2 100 hg38.150200.bed.split4899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split49 0 1 2 100 hg38.150200.bed.split49.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split490 0 1 2 100 hg38.150200.bed.split490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4900 0 1 2 100 hg38.150200.bed.split4900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4901 0 1 2 100 hg38.150200.bed.split4901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4902 0 1 2 100 hg38.150200.bed.split4902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4903 0 1 2 100 hg38.150200.bed.split4903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4904 0 1 2 100 hg38.150200.bed.split4904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4905 0 1 2 100 hg38.150200.bed.split4905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4906 0 1 2 100 hg38.150200.bed.split4906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4907 0 1 2 100 hg38.150200.bed.split4907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4908 0 1 2 100 hg38.150200.bed.split4908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4909 0 1 2 100 hg38.150200.bed.split4909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split491 0 1 2 100 hg38.150200.bed.split491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4910 0 1 2 100 hg38.150200.bed.split4910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4911 0 1 2 100 hg38.150200.bed.split4911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4912 0 1 2 100 hg38.150200.bed.split4912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4913 0 1 2 100 hg38.150200.bed.split4913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4914 0 1 2 100 hg38.150200.bed.split4914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4915 0 1 2 100 hg38.150200.bed.split4915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4916 0 1 2 100 hg38.150200.bed.split4916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4917 0 1 2 100 hg38.150200.bed.split4917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4918 0 1 2 100 hg38.150200.bed.split4918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4919 0 1 2 100 hg38.150200.bed.split4919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split492 0 1 2 100 hg38.150200.bed.split492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4920 0 1 2 100 hg38.150200.bed.split4920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4921 0 1 2 100 hg38.150200.bed.split4921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4922 0 1 2 100 hg38.150200.bed.split4922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4923 0 1 2 100 hg38.150200.bed.split4923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4924 0 1 2 100 hg38.150200.bed.split4924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4925 0 1 2 100 hg38.150200.bed.split4925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4926 0 1 2 100 hg38.150200.bed.split4926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4927 0 1 2 100 hg38.150200.bed.split4927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4928 0 1 2 100 hg38.150200.bed.split4928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4929 0 1 2 100 hg38.150200.bed.split4929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split493 0 1 2 100 hg38.150200.bed.split493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4930 0 1 2 100 hg38.150200.bed.split4930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4931 0 1 2 100 hg38.150200.bed.split4931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4932 0 1 2 100 hg38.150200.bed.split4932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4933 0 1 2 100 hg38.150200.bed.split4933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4934 0 1 2 100 hg38.150200.bed.split4934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4935 0 1 2 100 hg38.150200.bed.split4935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4936 0 1 2 100 hg38.150200.bed.split4936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4937 0 1 2 100 hg38.150200.bed.split4937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4938 0 1 2 100 hg38.150200.bed.split4938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4939 0 1 2 100 hg38.150200.bed.split4939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split494 0 1 2 100 hg38.150200.bed.split494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4940 0 1 2 100 hg38.150200.bed.split4940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4941 0 1 2 100 hg38.150200.bed.split4941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4942 0 1 2 100 hg38.150200.bed.split4942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4943 0 1 2 100 hg38.150200.bed.split4943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4944 0 1 2 100 hg38.150200.bed.split4944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4945 0 1 2 100 hg38.150200.bed.split4945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4946 0 1 2 100 hg38.150200.bed.split4946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4947 0 1 2 100 hg38.150200.bed.split4947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4948 0 1 2 100 hg38.150200.bed.split4948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4949 0 1 2 100 hg38.150200.bed.split4949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split495 0 1 2 100 hg38.150200.bed.split495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4950 0 1 2 100 hg38.150200.bed.split4950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4951 0 1 2 100 hg38.150200.bed.split4951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4952 0 1 2 100 hg38.150200.bed.split4952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4953 0 1 2 100 hg38.150200.bed.split4953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4954 0 1 2 100 hg38.150200.bed.split4954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4955 0 1 2 100 hg38.150200.bed.split4955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4956 0 1 2 100 hg38.150200.bed.split4956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4957 0 1 2 100 hg38.150200.bed.split4957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4958 0 1 2 100 hg38.150200.bed.split4958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4959 0 1 2 100 hg38.150200.bed.split4959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split496 0 1 2 100 hg38.150200.bed.split496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4960 0 1 2 100 hg38.150200.bed.split4960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4961 0 1 2 100 hg38.150200.bed.split4961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4962 0 1 2 100 hg38.150200.bed.split4962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4963 0 1 2 100 hg38.150200.bed.split4963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4964 0 1 2 100 hg38.150200.bed.split4964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4965 0 1 2 100 hg38.150200.bed.split4965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4966 0 1 2 100 hg38.150200.bed.split4966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4967 0 1 2 100 hg38.150200.bed.split4967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4968 0 1 2 100 hg38.150200.bed.split4968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4969 0 1 2 100 hg38.150200.bed.split4969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split497 0 1 2 100 hg38.150200.bed.split497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4970 0 1 2 100 hg38.150200.bed.split4970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4971 0 1 2 100 hg38.150200.bed.split4971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4972 0 1 2 100 hg38.150200.bed.split4972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4973 0 1 2 100 hg38.150200.bed.split4973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4974 0 1 2 100 hg38.150200.bed.split4974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4975 0 1 2 100 hg38.150200.bed.split4975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4976 0 1 2 100 hg38.150200.bed.split4976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4977 0 1 2 100 hg38.150200.bed.split4977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4978 0 1 2 100 hg38.150200.bed.split4978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4979 0 1 2 100 hg38.150200.bed.split4979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split498 0 1 2 100 hg38.150200.bed.split498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4980 0 1 2 100 hg38.150200.bed.split4980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4981 0 1 2 100 hg38.150200.bed.split4981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4982 0 1 2 100 hg38.150200.bed.split4982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4983 0 1 2 100 hg38.150200.bed.split4983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4984 0 1 2 100 hg38.150200.bed.split4984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4985 0 1 2 100 hg38.150200.bed.split4985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4986 0 1 2 100 hg38.150200.bed.split4986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4987 0 1 2 100 hg38.150200.bed.split4987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4988 0 1 2 100 hg38.150200.bed.split4988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4989 0 1 2 100 hg38.150200.bed.split4989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split499 0 1 2 100 hg38.150200.bed.split499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4990 0 1 2 100 hg38.150200.bed.split4990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4991 0 1 2 100 hg38.150200.bed.split4991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4992 0 1 2 100 hg38.150200.bed.split4992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4993 0 1 2 100 hg38.150200.bed.split4993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4994 0 1 2 100 hg38.150200.bed.split4994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4995 0 1 2 100 hg38.150200.bed.split4995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4996 0 1 2 100 hg38.150200.bed.split4996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4997 0 1 2 100 hg38.150200.bed.split4997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4998 0 1 2 100 hg38.150200.bed.split4998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split4999 0 1 2 100 hg38.150200.bed.split4999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5 0 1 2 100 hg38.150200.bed.split5.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split50 0 1 2 100 hg38.150200.bed.split50.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split500 0 1 2 100 hg38.150200.bed.split500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5000 0 1 2 100 hg38.150200.bed.split5000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5001 0 1 2 100 hg38.150200.bed.split5001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5002 0 1 2 100 hg38.150200.bed.split5002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5003 0 1 2 100 hg38.150200.bed.split5003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5004 0 1 2 100 hg38.150200.bed.split5004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5005 0 1 2 100 hg38.150200.bed.split5005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5006 0 1 2 100 hg38.150200.bed.split5006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5007 0 1 2 100 hg38.150200.bed.split5007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5008 0 1 2 100 hg38.150200.bed.split5008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5009 0 1 2 100 hg38.150200.bed.split5009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split501 0 1 2 100 hg38.150200.bed.split501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5010 0 1 2 100 hg38.150200.bed.split5010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5011 0 1 2 100 hg38.150200.bed.split5011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5012 0 1 2 100 hg38.150200.bed.split5012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5013 0 1 2 100 hg38.150200.bed.split5013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5014 0 1 2 100 hg38.150200.bed.split5014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5015 0 1 2 100 hg38.150200.bed.split5015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5016 0 1 2 100 hg38.150200.bed.split5016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5017 0 1 2 100 hg38.150200.bed.split5017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5018 0 1 2 100 hg38.150200.bed.split5018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5019 0 1 2 100 hg38.150200.bed.split5019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split502 0 1 2 100 hg38.150200.bed.split502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5020 0 1 2 100 hg38.150200.bed.split5020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5021 0 1 2 100 hg38.150200.bed.split5021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5022 0 1 2 100 hg38.150200.bed.split5022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5023 0 1 2 100 hg38.150200.bed.split5023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5024 0 1 2 100 hg38.150200.bed.split5024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5025 0 1 2 100 hg38.150200.bed.split5025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5026 0 1 2 100 hg38.150200.bed.split5026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5027 0 1 2 100 hg38.150200.bed.split5027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5028 0 1 2 100 hg38.150200.bed.split5028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5029 0 1 2 100 hg38.150200.bed.split5029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split503 0 1 2 100 hg38.150200.bed.split503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5030 0 1 2 100 hg38.150200.bed.split5030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5031 0 1 2 100 hg38.150200.bed.split5031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5032 0 1 2 100 hg38.150200.bed.split5032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5033 0 1 2 100 hg38.150200.bed.split5033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5034 0 1 2 100 hg38.150200.bed.split5034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5035 0 1 2 100 hg38.150200.bed.split5035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5036 0 1 2 100 hg38.150200.bed.split5036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5037 0 1 2 100 hg38.150200.bed.split5037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5038 0 1 2 100 hg38.150200.bed.split5038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5039 0 1 2 100 hg38.150200.bed.split5039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split504 0 1 2 100 hg38.150200.bed.split504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5040 0 1 2 100 hg38.150200.bed.split5040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5041 0 1 2 100 hg38.150200.bed.split5041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5042 0 1 2 100 hg38.150200.bed.split5042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5043 0 1 2 100 hg38.150200.bed.split5043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5044 0 1 2 100 hg38.150200.bed.split5044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5045 0 1 2 100 hg38.150200.bed.split5045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5046 0 1 2 100 hg38.150200.bed.split5046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5047 0 1 2 100 hg38.150200.bed.split5047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5048 0 1 2 100 hg38.150200.bed.split5048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5049 0 1 2 100 hg38.150200.bed.split5049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split505 0 1 2 100 hg38.150200.bed.split505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5050 0 1 2 100 hg38.150200.bed.split5050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5051 0 1 2 100 hg38.150200.bed.split5051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5052 0 1 2 100 hg38.150200.bed.split5052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5053 0 1 2 100 hg38.150200.bed.split5053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5054 0 1 2 100 hg38.150200.bed.split5054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5055 0 1 2 100 hg38.150200.bed.split5055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5056 0 1 2 100 hg38.150200.bed.split5056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5057 0 1 2 100 hg38.150200.bed.split5057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5058 0 1 2 100 hg38.150200.bed.split5058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5059 0 1 2 100 hg38.150200.bed.split5059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split506 0 1 2 100 hg38.150200.bed.split506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5060 0 1 2 100 hg38.150200.bed.split5060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5061 0 1 2 100 hg38.150200.bed.split5061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5062 0 1 2 100 hg38.150200.bed.split5062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5063 0 1 2 100 hg38.150200.bed.split5063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5064 0 1 2 100 hg38.150200.bed.split5064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5065 0 1 2 100 hg38.150200.bed.split5065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5066 0 1 2 100 hg38.150200.bed.split5066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5067 0 1 2 100 hg38.150200.bed.split5067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5068 0 1 2 100 hg38.150200.bed.split5068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5069 0 1 2 100 hg38.150200.bed.split5069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split507 0 1 2 100 hg38.150200.bed.split507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5070 0 1 2 100 hg38.150200.bed.split5070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5071 0 1 2 100 hg38.150200.bed.split5071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5072 0 1 2 100 hg38.150200.bed.split5072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5073 0 1 2 100 hg38.150200.bed.split5073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5074 0 1 2 100 hg38.150200.bed.split5074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5075 0 1 2 100 hg38.150200.bed.split5075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5076 0 1 2 100 hg38.150200.bed.split5076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5077 0 1 2 100 hg38.150200.bed.split5077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5078 0 1 2 100 hg38.150200.bed.split5078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5079 0 1 2 100 hg38.150200.bed.split5079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split508 0 1 2 100 hg38.150200.bed.split508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5080 0 1 2 100 hg38.150200.bed.split5080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5081 0 1 2 100 hg38.150200.bed.split5081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5082 0 1 2 100 hg38.150200.bed.split5082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5083 0 1 2 100 hg38.150200.bed.split5083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5084 0 1 2 100 hg38.150200.bed.split5084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5085 0 1 2 100 hg38.150200.bed.split5085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5086 0 1 2 100 hg38.150200.bed.split5086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5087 0 1 2 100 hg38.150200.bed.split5087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5088 0 1 2 100 hg38.150200.bed.split5088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5089 0 1 2 100 hg38.150200.bed.split5089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split509 0 1 2 100 hg38.150200.bed.split509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5090 0 1 2 100 hg38.150200.bed.split5090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5091 0 1 2 100 hg38.150200.bed.split5091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5092 0 1 2 100 hg38.150200.bed.split5092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5093 0 1 2 100 hg38.150200.bed.split5093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5094 0 1 2 100 hg38.150200.bed.split5094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5095 0 1 2 100 hg38.150200.bed.split5095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5096 0 1 2 100 hg38.150200.bed.split5096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5097 0 1 2 100 hg38.150200.bed.split5097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5098 0 1 2 100 hg38.150200.bed.split5098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5099 0 1 2 100 hg38.150200.bed.split5099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split51 0 1 2 100 hg38.150200.bed.split51.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split510 0 1 2 100 hg38.150200.bed.split510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5100 0 1 2 100 hg38.150200.bed.split5100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5101 0 1 2 100 hg38.150200.bed.split5101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5102 0 1 2 100 hg38.150200.bed.split5102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5103 0 1 2 100 hg38.150200.bed.split5103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5104 0 1 2 100 hg38.150200.bed.split5104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5105 0 1 2 100 hg38.150200.bed.split5105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5106 0 1 2 100 hg38.150200.bed.split5106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5107 0 1 2 100 hg38.150200.bed.split5107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5108 0 1 2 100 hg38.150200.bed.split5108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5109 0 1 2 100 hg38.150200.bed.split5109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split511 0 1 2 100 hg38.150200.bed.split511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5110 0 1 2 100 hg38.150200.bed.split5110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5111 0 1 2 100 hg38.150200.bed.split5111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5112 0 1 2 100 hg38.150200.bed.split5112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5113 0 1 2 100 hg38.150200.bed.split5113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5114 0 1 2 100 hg38.150200.bed.split5114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5115 0 1 2 100 hg38.150200.bed.split5115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5116 0 1 2 100 hg38.150200.bed.split5116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5117 0 1 2 100 hg38.150200.bed.split5117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5118 0 1 2 100 hg38.150200.bed.split5118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5119 0 1 2 100 hg38.150200.bed.split5119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split512 0 1 2 100 hg38.150200.bed.split512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5120 0 1 2 100 hg38.150200.bed.split5120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5121 0 1 2 100 hg38.150200.bed.split5121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5122 0 1 2 100 hg38.150200.bed.split5122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5123 0 1 2 100 hg38.150200.bed.split5123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5124 0 1 2 100 hg38.150200.bed.split5124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5125 0 1 2 100 hg38.150200.bed.split5125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5126 0 1 2 100 hg38.150200.bed.split5126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5127 0 1 2 100 hg38.150200.bed.split5127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5128 0 1 2 100 hg38.150200.bed.split5128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5129 0 1 2 100 hg38.150200.bed.split5129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split513 0 1 2 100 hg38.150200.bed.split513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5130 0 1 2 100 hg38.150200.bed.split5130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5131 0 1 2 100 hg38.150200.bed.split5131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5132 0 1 2 100 hg38.150200.bed.split5132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5133 0 1 2 100 hg38.150200.bed.split5133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5134 0 1 2 100 hg38.150200.bed.split5134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5135 0 1 2 100 hg38.150200.bed.split5135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5136 0 1 2 100 hg38.150200.bed.split5136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5137 0 1 2 100 hg38.150200.bed.split5137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5138 0 1 2 100 hg38.150200.bed.split5138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5139 0 1 2 100 hg38.150200.bed.split5139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split514 0 1 2 100 hg38.150200.bed.split514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5140 0 1 2 100 hg38.150200.bed.split5140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5141 0 1 2 100 hg38.150200.bed.split5141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5142 0 1 2 100 hg38.150200.bed.split5142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5143 0 1 2 100 hg38.150200.bed.split5143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5144 0 1 2 100 hg38.150200.bed.split5144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5145 0 1 2 100 hg38.150200.bed.split5145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5146 0 1 2 100 hg38.150200.bed.split5146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5147 0 1 2 100 hg38.150200.bed.split5147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5148 0 1 2 100 hg38.150200.bed.split5148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5149 0 1 2 100 hg38.150200.bed.split5149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split515 0 1 2 100 hg38.150200.bed.split515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5150 0 1 2 100 hg38.150200.bed.split5150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5151 0 1 2 100 hg38.150200.bed.split5151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5152 0 1 2 100 hg38.150200.bed.split5152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5153 0 1 2 100 hg38.150200.bed.split5153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5154 0 1 2 100 hg38.150200.bed.split5154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5155 0 1 2 100 hg38.150200.bed.split5155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5156 0 1 2 100 hg38.150200.bed.split5156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5157 0 1 2 100 hg38.150200.bed.split5157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5158 0 1 2 100 hg38.150200.bed.split5158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5159 0 1 2 100 hg38.150200.bed.split5159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split516 0 1 2 100 hg38.150200.bed.split516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5160 0 1 2 100 hg38.150200.bed.split5160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5161 0 1 2 100 hg38.150200.bed.split5161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5162 0 1 2 100 hg38.150200.bed.split5162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5163 0 1 2 100 hg38.150200.bed.split5163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5164 0 1 2 100 hg38.150200.bed.split5164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5165 0 1 2 100 hg38.150200.bed.split5165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5166 0 1 2 100 hg38.150200.bed.split5166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5167 0 1 2 100 hg38.150200.bed.split5167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5168 0 1 2 100 hg38.150200.bed.split5168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5169 0 1 2 100 hg38.150200.bed.split5169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split517 0 1 2 100 hg38.150200.bed.split517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5170 0 1 2 100 hg38.150200.bed.split5170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5171 0 1 2 100 hg38.150200.bed.split5171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5172 0 1 2 100 hg38.150200.bed.split5172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5173 0 1 2 100 hg38.150200.bed.split5173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5174 0 1 2 100 hg38.150200.bed.split5174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5175 0 1 2 100 hg38.150200.bed.split5175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5176 0 1 2 100 hg38.150200.bed.split5176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5177 0 1 2 100 hg38.150200.bed.split5177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5178 0 1 2 100 hg38.150200.bed.split5178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5179 0 1 2 100 hg38.150200.bed.split5179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split518 0 1 2 100 hg38.150200.bed.split518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5180 0 1 2 100 hg38.150200.bed.split5180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5181 0 1 2 100 hg38.150200.bed.split5181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5182 0 1 2 100 hg38.150200.bed.split5182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5183 0 1 2 100 hg38.150200.bed.split5183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5184 0 1 2 100 hg38.150200.bed.split5184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5185 0 1 2 100 hg38.150200.bed.split5185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5186 0 1 2 100 hg38.150200.bed.split5186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5187 0 1 2 100 hg38.150200.bed.split5187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5188 0 1 2 100 hg38.150200.bed.split5188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5189 0 1 2 100 hg38.150200.bed.split5189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split519 0 1 2 100 hg38.150200.bed.split519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5190 0 1 2 100 hg38.150200.bed.split5190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5191 0 1 2 100 hg38.150200.bed.split5191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5192 0 1 2 100 hg38.150200.bed.split5192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5193 0 1 2 100 hg38.150200.bed.split5193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5194 0 1 2 100 hg38.150200.bed.split5194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5195 0 1 2 100 hg38.150200.bed.split5195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5196 0 1 2 100 hg38.150200.bed.split5196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5197 0 1 2 100 hg38.150200.bed.split5197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5198 0 1 2 100 hg38.150200.bed.split5198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5199 0 1 2 100 hg38.150200.bed.split5199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split52 0 1 2 100 hg38.150200.bed.split52.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split520 0 1 2 100 hg38.150200.bed.split520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5200 0 1 2 100 hg38.150200.bed.split5200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5201 0 1 2 100 hg38.150200.bed.split5201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5202 0 1 2 100 hg38.150200.bed.split5202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5203 0 1 2 100 hg38.150200.bed.split5203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5204 0 1 2 100 hg38.150200.bed.split5204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5205 0 1 2 100 hg38.150200.bed.split5205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5206 0 1 2 100 hg38.150200.bed.split5206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5207 0 1 2 100 hg38.150200.bed.split5207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5208 0 1 2 100 hg38.150200.bed.split5208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5209 0 1 2 100 hg38.150200.bed.split5209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split521 0 1 2 100 hg38.150200.bed.split521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5210 0 1 2 100 hg38.150200.bed.split5210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5211 0 1 2 100 hg38.150200.bed.split5211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5212 0 1 2 100 hg38.150200.bed.split5212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5213 0 1 2 100 hg38.150200.bed.split5213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5214 0 1 2 100 hg38.150200.bed.split5214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5215 0 1 2 100 hg38.150200.bed.split5215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5216 0 1 2 100 hg38.150200.bed.split5216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5217 0 1 2 100 hg38.150200.bed.split5217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5218 0 1 2 100 hg38.150200.bed.split5218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5219 0 1 2 100 hg38.150200.bed.split5219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split522 0 1 2 100 hg38.150200.bed.split522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5220 0 1 2 100 hg38.150200.bed.split5220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5221 0 1 2 100 hg38.150200.bed.split5221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5222 0 1 2 100 hg38.150200.bed.split5222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5223 0 1 2 100 hg38.150200.bed.split5223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5224 0 1 2 100 hg38.150200.bed.split5224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5225 0 1 2 100 hg38.150200.bed.split5225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5226 0 1 2 100 hg38.150200.bed.split5226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5227 0 1 2 100 hg38.150200.bed.split5227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5228 0 1 2 100 hg38.150200.bed.split5228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5229 0 1 2 100 hg38.150200.bed.split5229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split523 0 1 2 100 hg38.150200.bed.split523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5230 0 1 2 100 hg38.150200.bed.split5230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5231 0 1 2 100 hg38.150200.bed.split5231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5232 0 1 2 100 hg38.150200.bed.split5232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5233 0 1 2 100 hg38.150200.bed.split5233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5234 0 1 2 100 hg38.150200.bed.split5234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5235 0 1 2 100 hg38.150200.bed.split5235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5236 0 1 2 100 hg38.150200.bed.split5236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5237 0 1 2 100 hg38.150200.bed.split5237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5238 0 1 2 100 hg38.150200.bed.split5238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5239 0 1 2 100 hg38.150200.bed.split5239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split524 0 1 2 100 hg38.150200.bed.split524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5240 0 1 2 100 hg38.150200.bed.split5240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5241 0 1 2 100 hg38.150200.bed.split5241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5242 0 1 2 100 hg38.150200.bed.split5242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5243 0 1 2 100 hg38.150200.bed.split5243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5244 0 1 2 100 hg38.150200.bed.split5244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5245 0 1 2 100 hg38.150200.bed.split5245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5246 0 1 2 100 hg38.150200.bed.split5246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5247 0 1 2 100 hg38.150200.bed.split5247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5248 0 1 2 100 hg38.150200.bed.split5248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5249 0 1 2 100 hg38.150200.bed.split5249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split525 0 1 2 100 hg38.150200.bed.split525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5250 0 1 2 100 hg38.150200.bed.split5250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5251 0 1 2 100 hg38.150200.bed.split5251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5252 0 1 2 100 hg38.150200.bed.split5252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5253 0 1 2 100 hg38.150200.bed.split5253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5254 0 1 2 100 hg38.150200.bed.split5254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5255 0 1 2 100 hg38.150200.bed.split5255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5256 0 1 2 100 hg38.150200.bed.split5256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5257 0 1 2 100 hg38.150200.bed.split5257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5258 0 1 2 100 hg38.150200.bed.split5258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5259 0 1 2 100 hg38.150200.bed.split5259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split526 0 1 2 100 hg38.150200.bed.split526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5260 0 1 2 100 hg38.150200.bed.split5260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5261 0 1 2 100 hg38.150200.bed.split5261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5262 0 1 2 100 hg38.150200.bed.split5262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5263 0 1 2 100 hg38.150200.bed.split5263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5264 0 1 2 100 hg38.150200.bed.split5264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5265 0 1 2 100 hg38.150200.bed.split5265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5266 0 1 2 100 hg38.150200.bed.split5266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5267 0 1 2 100 hg38.150200.bed.split5267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5268 0 1 2 100 hg38.150200.bed.split5268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5269 0 1 2 100 hg38.150200.bed.split5269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split527 0 1 2 100 hg38.150200.bed.split527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5270 0 1 2 100 hg38.150200.bed.split5270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5271 0 1 2 100 hg38.150200.bed.split5271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5272 0 1 2 100 hg38.150200.bed.split5272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5273 0 1 2 100 hg38.150200.bed.split5273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5274 0 1 2 100 hg38.150200.bed.split5274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5275 0 1 2 100 hg38.150200.bed.split5275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5276 0 1 2 100 hg38.150200.bed.split5276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5277 0 1 2 100 hg38.150200.bed.split5277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5278 0 1 2 100 hg38.150200.bed.split5278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5279 0 1 2 100 hg38.150200.bed.split5279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split528 0 1 2 100 hg38.150200.bed.split528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5280 0 1 2 100 hg38.150200.bed.split5280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5281 0 1 2 100 hg38.150200.bed.split5281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5282 0 1 2 100 hg38.150200.bed.split5282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5283 0 1 2 100 hg38.150200.bed.split5283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5284 0 1 2 100 hg38.150200.bed.split5284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5285 0 1 2 100 hg38.150200.bed.split5285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5286 0 1 2 100 hg38.150200.bed.split5286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5287 0 1 2 100 hg38.150200.bed.split5287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5288 0 1 2 100 hg38.150200.bed.split5288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5289 0 1 2 100 hg38.150200.bed.split5289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split529 0 1 2 100 hg38.150200.bed.split529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5290 0 1 2 100 hg38.150200.bed.split5290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5291 0 1 2 100 hg38.150200.bed.split5291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5292 0 1 2 100 hg38.150200.bed.split5292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5293 0 1 2 100 hg38.150200.bed.split5293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5294 0 1 2 100 hg38.150200.bed.split5294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5295 0 1 2 100 hg38.150200.bed.split5295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5296 0 1 2 100 hg38.150200.bed.split5296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5297 0 1 2 100 hg38.150200.bed.split5297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5298 0 1 2 100 hg38.150200.bed.split5298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5299 0 1 2 100 hg38.150200.bed.split5299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split53 0 1 2 100 hg38.150200.bed.split53.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split530 0 1 2 100 hg38.150200.bed.split530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5300 0 1 2 100 hg38.150200.bed.split5300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5301 0 1 2 100 hg38.150200.bed.split5301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5302 0 1 2 100 hg38.150200.bed.split5302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5303 0 1 2 100 hg38.150200.bed.split5303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5304 0 1 2 100 hg38.150200.bed.split5304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5305 0 1 2 100 hg38.150200.bed.split5305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5306 0 1 2 100 hg38.150200.bed.split5306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5307 0 1 2 100 hg38.150200.bed.split5307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5308 0 1 2 100 hg38.150200.bed.split5308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5309 0 1 2 100 hg38.150200.bed.split5309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split531 0 1 2 100 hg38.150200.bed.split531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5310 0 1 2 100 hg38.150200.bed.split5310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5311 0 1 2 100 hg38.150200.bed.split5311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5312 0 1 2 100 hg38.150200.bed.split5312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5313 0 1 2 100 hg38.150200.bed.split5313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5314 0 1 2 100 hg38.150200.bed.split5314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5315 0 1 2 100 hg38.150200.bed.split5315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5316 0 1 2 100 hg38.150200.bed.split5316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5317 0 1 2 100 hg38.150200.bed.split5317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5318 0 1 2 100 hg38.150200.bed.split5318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5319 0 1 2 100 hg38.150200.bed.split5319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split532 0 1 2 100 hg38.150200.bed.split532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5320 0 1 2 100 hg38.150200.bed.split5320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5321 0 1 2 100 hg38.150200.bed.split5321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5322 0 1 2 100 hg38.150200.bed.split5322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5323 0 1 2 100 hg38.150200.bed.split5323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5324 0 1 2 100 hg38.150200.bed.split5324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5325 0 1 2 100 hg38.150200.bed.split5325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5326 0 1 2 100 hg38.150200.bed.split5326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5327 0 1 2 100 hg38.150200.bed.split5327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5328 0 1 2 100 hg38.150200.bed.split5328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5329 0 1 2 100 hg38.150200.bed.split5329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split533 0 1 2 100 hg38.150200.bed.split533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5330 0 1 2 100 hg38.150200.bed.split5330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5331 0 1 2 100 hg38.150200.bed.split5331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5332 0 1 2 100 hg38.150200.bed.split5332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5333 0 1 2 100 hg38.150200.bed.split5333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5334 0 1 2 100 hg38.150200.bed.split5334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5335 0 1 2 100 hg38.150200.bed.split5335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5336 0 1 2 100 hg38.150200.bed.split5336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5337 0 1 2 100 hg38.150200.bed.split5337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5338 0 1 2 100 hg38.150200.bed.split5338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5339 0 1 2 100 hg38.150200.bed.split5339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split534 0 1 2 100 hg38.150200.bed.split534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5340 0 1 2 100 hg38.150200.bed.split5340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5341 0 1 2 100 hg38.150200.bed.split5341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5342 0 1 2 100 hg38.150200.bed.split5342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5343 0 1 2 100 hg38.150200.bed.split5343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5344 0 1 2 100 hg38.150200.bed.split5344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5345 0 1 2 100 hg38.150200.bed.split5345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5346 0 1 2 100 hg38.150200.bed.split5346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5347 0 1 2 100 hg38.150200.bed.split5347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5348 0 1 2 100 hg38.150200.bed.split5348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5349 0 1 2 100 hg38.150200.bed.split5349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split535 0 1 2 100 hg38.150200.bed.split535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5350 0 1 2 100 hg38.150200.bed.split5350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5351 0 1 2 100 hg38.150200.bed.split5351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5352 0 1 2 100 hg38.150200.bed.split5352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5353 0 1 2 100 hg38.150200.bed.split5353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5354 0 1 2 100 hg38.150200.bed.split5354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5355 0 1 2 100 hg38.150200.bed.split5355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5356 0 1 2 100 hg38.150200.bed.split5356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5357 0 1 2 100 hg38.150200.bed.split5357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5358 0 1 2 100 hg38.150200.bed.split5358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5359 0 1 2 100 hg38.150200.bed.split5359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split536 0 1 2 100 hg38.150200.bed.split536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5360 0 1 2 100 hg38.150200.bed.split5360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5361 0 1 2 100 hg38.150200.bed.split5361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5362 0 1 2 100 hg38.150200.bed.split5362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5363 0 1 2 100 hg38.150200.bed.split5363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5364 0 1 2 100 hg38.150200.bed.split5364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5365 0 1 2 100 hg38.150200.bed.split5365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5366 0 1 2 100 hg38.150200.bed.split5366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5367 0 1 2 100 hg38.150200.bed.split5367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5368 0 1 2 100 hg38.150200.bed.split5368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5369 0 1 2 100 hg38.150200.bed.split5369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split537 0 1 2 100 hg38.150200.bed.split537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5370 0 1 2 100 hg38.150200.bed.split5370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5371 0 1 2 100 hg38.150200.bed.split5371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5372 0 1 2 100 hg38.150200.bed.split5372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5373 0 1 2 100 hg38.150200.bed.split5373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5374 0 1 2 100 hg38.150200.bed.split5374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5375 0 1 2 100 hg38.150200.bed.split5375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5376 0 1 2 100 hg38.150200.bed.split5376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5377 0 1 2 100 hg38.150200.bed.split5377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5378 0 1 2 100 hg38.150200.bed.split5378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5379 0 1 2 100 hg38.150200.bed.split5379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split538 0 1 2 100 hg38.150200.bed.split538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5380 0 1 2 100 hg38.150200.bed.split5380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5381 0 1 2 100 hg38.150200.bed.split5381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5382 0 1 2 100 hg38.150200.bed.split5382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5383 0 1 2 100 hg38.150200.bed.split5383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5384 0 1 2 100 hg38.150200.bed.split5384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5385 0 1 2 100 hg38.150200.bed.split5385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5386 0 1 2 100 hg38.150200.bed.split5386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5387 0 1 2 100 hg38.150200.bed.split5387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5388 0 1 2 100 hg38.150200.bed.split5388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5389 0 1 2 100 hg38.150200.bed.split5389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split539 0 1 2 100 hg38.150200.bed.split539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5390 0 1 2 100 hg38.150200.bed.split5390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5391 0 1 2 100 hg38.150200.bed.split5391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5392 0 1 2 100 hg38.150200.bed.split5392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5393 0 1 2 100 hg38.150200.bed.split5393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5394 0 1 2 100 hg38.150200.bed.split5394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5395 0 1 2 100 hg38.150200.bed.split5395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5396 0 1 2 100 hg38.150200.bed.split5396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5397 0 1 2 100 hg38.150200.bed.split5397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5398 0 1 2 100 hg38.150200.bed.split5398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5399 0 1 2 100 hg38.150200.bed.split5399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split54 0 1 2 100 hg38.150200.bed.split54.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split540 0 1 2 100 hg38.150200.bed.split540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5400 0 1 2 100 hg38.150200.bed.split5400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5401 0 1 2 100 hg38.150200.bed.split5401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5402 0 1 2 100 hg38.150200.bed.split5402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5403 0 1 2 100 hg38.150200.bed.split5403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5404 0 1 2 100 hg38.150200.bed.split5404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5405 0 1 2 100 hg38.150200.bed.split5405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5406 0 1 2 100 hg38.150200.bed.split5406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5407 0 1 2 100 hg38.150200.bed.split5407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5408 0 1 2 100 hg38.150200.bed.split5408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5409 0 1 2 100 hg38.150200.bed.split5409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split541 0 1 2 100 hg38.150200.bed.split541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5410 0 1 2 100 hg38.150200.bed.split5410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5411 0 1 2 100 hg38.150200.bed.split5411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5412 0 1 2 100 hg38.150200.bed.split5412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5413 0 1 2 100 hg38.150200.bed.split5413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5414 0 1 2 100 hg38.150200.bed.split5414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5415 0 1 2 100 hg38.150200.bed.split5415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5416 0 1 2 100 hg38.150200.bed.split5416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5417 0 1 2 100 hg38.150200.bed.split5417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5418 0 1 2 100 hg38.150200.bed.split5418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5419 0 1 2 100 hg38.150200.bed.split5419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split542 0 1 2 100 hg38.150200.bed.split542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5420 0 1 2 100 hg38.150200.bed.split5420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5421 0 1 2 100 hg38.150200.bed.split5421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5422 0 1 2 100 hg38.150200.bed.split5422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5423 0 1 2 100 hg38.150200.bed.split5423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5424 0 1 2 100 hg38.150200.bed.split5424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5425 0 1 2 100 hg38.150200.bed.split5425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5426 0 1 2 100 hg38.150200.bed.split5426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5427 0 1 2 100 hg38.150200.bed.split5427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5428 0 1 2 100 hg38.150200.bed.split5428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5429 0 1 2 100 hg38.150200.bed.split5429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split543 0 1 2 100 hg38.150200.bed.split543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5430 0 1 2 100 hg38.150200.bed.split5430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5431 0 1 2 100 hg38.150200.bed.split5431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5432 0 1 2 100 hg38.150200.bed.split5432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5433 0 1 2 100 hg38.150200.bed.split5433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5434 0 1 2 100 hg38.150200.bed.split5434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5435 0 1 2 100 hg38.150200.bed.split5435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5436 0 1 2 100 hg38.150200.bed.split5436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5437 0 1 2 100 hg38.150200.bed.split5437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5438 0 1 2 100 hg38.150200.bed.split5438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5439 0 1 2 100 hg38.150200.bed.split5439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split544 0 1 2 100 hg38.150200.bed.split544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5440 0 1 2 100 hg38.150200.bed.split5440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5441 0 1 2 100 hg38.150200.bed.split5441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5442 0 1 2 100 hg38.150200.bed.split5442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5443 0 1 2 100 hg38.150200.bed.split5443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5444 0 1 2 100 hg38.150200.bed.split5444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5445 0 1 2 100 hg38.150200.bed.split5445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5446 0 1 2 100 hg38.150200.bed.split5446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5447 0 1 2 100 hg38.150200.bed.split5447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5448 0 1 2 100 hg38.150200.bed.split5448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5449 0 1 2 100 hg38.150200.bed.split5449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split545 0 1 2 100 hg38.150200.bed.split545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5450 0 1 2 100 hg38.150200.bed.split5450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5451 0 1 2 100 hg38.150200.bed.split5451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5452 0 1 2 100 hg38.150200.bed.split5452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5453 0 1 2 100 hg38.150200.bed.split5453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5454 0 1 2 100 hg38.150200.bed.split5454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5455 0 1 2 100 hg38.150200.bed.split5455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5456 0 1 2 100 hg38.150200.bed.split5456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5457 0 1 2 100 hg38.150200.bed.split5457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5458 0 1 2 100 hg38.150200.bed.split5458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5459 0 1 2 100 hg38.150200.bed.split5459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split546 0 1 2 100 hg38.150200.bed.split546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5460 0 1 2 100 hg38.150200.bed.split5460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5461 0 1 2 100 hg38.150200.bed.split5461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5462 0 1 2 100 hg38.150200.bed.split5462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5463 0 1 2 100 hg38.150200.bed.split5463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5464 0 1 2 100 hg38.150200.bed.split5464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5465 0 1 2 100 hg38.150200.bed.split5465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5466 0 1 2 100 hg38.150200.bed.split5466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5467 0 1 2 100 hg38.150200.bed.split5467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5468 0 1 2 100 hg38.150200.bed.split5468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5469 0 1 2 100 hg38.150200.bed.split5469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split547 0 1 2 100 hg38.150200.bed.split547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5470 0 1 2 100 hg38.150200.bed.split5470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5471 0 1 2 100 hg38.150200.bed.split5471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5472 0 1 2 100 hg38.150200.bed.split5472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5473 0 1 2 100 hg38.150200.bed.split5473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5474 0 1 2 100 hg38.150200.bed.split5474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5475 0 1 2 100 hg38.150200.bed.split5475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5476 0 1 2 100 hg38.150200.bed.split5476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5477 0 1 2 100 hg38.150200.bed.split5477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5478 0 1 2 100 hg38.150200.bed.split5478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5479 0 1 2 100 hg38.150200.bed.split5479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split548 0 1 2 100 hg38.150200.bed.split548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5480 0 1 2 100 hg38.150200.bed.split5480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5481 0 1 2 100 hg38.150200.bed.split5481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5482 0 1 2 100 hg38.150200.bed.split5482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5483 0 1 2 100 hg38.150200.bed.split5483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5484 0 1 2 100 hg38.150200.bed.split5484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5485 0 1 2 100 hg38.150200.bed.split5485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5486 0 1 2 100 hg38.150200.bed.split5486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5487 0 1 2 100 hg38.150200.bed.split5487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5488 0 1 2 100 hg38.150200.bed.split5488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5489 0 1 2 100 hg38.150200.bed.split5489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split549 0 1 2 100 hg38.150200.bed.split549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5490 0 1 2 100 hg38.150200.bed.split5490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5491 0 1 2 100 hg38.150200.bed.split5491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5492 0 1 2 100 hg38.150200.bed.split5492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5493 0 1 2 100 hg38.150200.bed.split5493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5494 0 1 2 100 hg38.150200.bed.split5494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5495 0 1 2 100 hg38.150200.bed.split5495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5496 0 1 2 100 hg38.150200.bed.split5496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5497 0 1 2 100 hg38.150200.bed.split5497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5498 0 1 2 100 hg38.150200.bed.split5498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5499 0 1 2 100 hg38.150200.bed.split5499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split55 0 1 2 100 hg38.150200.bed.split55.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split550 0 1 2 100 hg38.150200.bed.split550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5500 0 1 2 100 hg38.150200.bed.split5500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5501 0 1 2 100 hg38.150200.bed.split5501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5502 0 1 2 100 hg38.150200.bed.split5502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5503 0 1 2 100 hg38.150200.bed.split5503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5504 0 1 2 100 hg38.150200.bed.split5504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5505 0 1 2 100 hg38.150200.bed.split5505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5506 0 1 2 100 hg38.150200.bed.split5506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5507 0 1 2 100 hg38.150200.bed.split5507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5508 0 1 2 100 hg38.150200.bed.split5508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5509 0 1 2 100 hg38.150200.bed.split5509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split551 0 1 2 100 hg38.150200.bed.split551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5510 0 1 2 100 hg38.150200.bed.split5510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5511 0 1 2 100 hg38.150200.bed.split5511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5512 0 1 2 100 hg38.150200.bed.split5512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5513 0 1 2 100 hg38.150200.bed.split5513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5514 0 1 2 100 hg38.150200.bed.split5514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5515 0 1 2 100 hg38.150200.bed.split5515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5516 0 1 2 100 hg38.150200.bed.split5516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5517 0 1 2 100 hg38.150200.bed.split5517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5518 0 1 2 100 hg38.150200.bed.split5518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5519 0 1 2 100 hg38.150200.bed.split5519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split552 0 1 2 100 hg38.150200.bed.split552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5520 0 1 2 100 hg38.150200.bed.split5520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5521 0 1 2 100 hg38.150200.bed.split5521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5522 0 1 2 100 hg38.150200.bed.split5522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5523 0 1 2 100 hg38.150200.bed.split5523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5524 0 1 2 100 hg38.150200.bed.split5524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5525 0 1 2 100 hg38.150200.bed.split5525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5526 0 1 2 100 hg38.150200.bed.split5526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5527 0 1 2 100 hg38.150200.bed.split5527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5528 0 1 2 100 hg38.150200.bed.split5528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5529 0 1 2 100 hg38.150200.bed.split5529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split553 0 1 2 100 hg38.150200.bed.split553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5530 0 1 2 100 hg38.150200.bed.split5530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5531 0 1 2 100 hg38.150200.bed.split5531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5532 0 1 2 100 hg38.150200.bed.split5532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5533 0 1 2 100 hg38.150200.bed.split5533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5534 0 1 2 100 hg38.150200.bed.split5534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5535 0 1 2 100 hg38.150200.bed.split5535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5536 0 1 2 100 hg38.150200.bed.split5536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5537 0 1 2 100 hg38.150200.bed.split5537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5538 0 1 2 100 hg38.150200.bed.split5538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5539 0 1 2 100 hg38.150200.bed.split5539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split554 0 1 2 100 hg38.150200.bed.split554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5540 0 1 2 100 hg38.150200.bed.split5540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5541 0 1 2 100 hg38.150200.bed.split5541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5542 0 1 2 100 hg38.150200.bed.split5542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5543 0 1 2 100 hg38.150200.bed.split5543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5544 0 1 2 100 hg38.150200.bed.split5544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5545 0 1 2 100 hg38.150200.bed.split5545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5546 0 1 2 100 hg38.150200.bed.split5546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5547 0 1 2 100 hg38.150200.bed.split5547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5548 0 1 2 100 hg38.150200.bed.split5548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5549 0 1 2 100 hg38.150200.bed.split5549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split555 0 1 2 100 hg38.150200.bed.split555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5550 0 1 2 100 hg38.150200.bed.split5550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5551 0 1 2 100 hg38.150200.bed.split5551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5552 0 1 2 100 hg38.150200.bed.split5552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5553 0 1 2 100 hg38.150200.bed.split5553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5554 0 1 2 100 hg38.150200.bed.split5554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5555 0 1 2 100 hg38.150200.bed.split5555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5556 0 1 2 100 hg38.150200.bed.split5556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5557 0 1 2 100 hg38.150200.bed.split5557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5558 0 1 2 100 hg38.150200.bed.split5558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5559 0 1 2 100 hg38.150200.bed.split5559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split556 0 1 2 100 hg38.150200.bed.split556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5560 0 1 2 100 hg38.150200.bed.split5560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5561 0 1 2 100 hg38.150200.bed.split5561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5562 0 1 2 100 hg38.150200.bed.split5562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5563 0 1 2 100 hg38.150200.bed.split5563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5564 0 1 2 100 hg38.150200.bed.split5564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5565 0 1 2 100 hg38.150200.bed.split5565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5566 0 1 2 100 hg38.150200.bed.split5566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5567 0 1 2 100 hg38.150200.bed.split5567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5568 0 1 2 100 hg38.150200.bed.split5568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5569 0 1 2 100 hg38.150200.bed.split5569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split557 0 1 2 100 hg38.150200.bed.split557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5570 0 1 2 100 hg38.150200.bed.split5570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5571 0 1 2 100 hg38.150200.bed.split5571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5572 0 1 2 100 hg38.150200.bed.split5572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5573 0 1 2 100 hg38.150200.bed.split5573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5574 0 1 2 100 hg38.150200.bed.split5574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5575 0 1 2 100 hg38.150200.bed.split5575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5576 0 1 2 100 hg38.150200.bed.split5576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5577 0 1 2 100 hg38.150200.bed.split5577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5578 0 1 2 100 hg38.150200.bed.split5578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5579 0 1 2 100 hg38.150200.bed.split5579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split558 0 1 2 100 hg38.150200.bed.split558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5580 0 1 2 100 hg38.150200.bed.split5580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5581 0 1 2 100 hg38.150200.bed.split5581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5582 0 1 2 100 hg38.150200.bed.split5582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5583 0 1 2 100 hg38.150200.bed.split5583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5584 0 1 2 100 hg38.150200.bed.split5584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5585 0 1 2 100 hg38.150200.bed.split5585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5586 0 1 2 100 hg38.150200.bed.split5586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5587 0 1 2 100 hg38.150200.bed.split5587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5588 0 1 2 100 hg38.150200.bed.split5588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5589 0 1 2 100 hg38.150200.bed.split5589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split559 0 1 2 100 hg38.150200.bed.split559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5590 0 1 2 100 hg38.150200.bed.split5590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5591 0 1 2 100 hg38.150200.bed.split5591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5592 0 1 2 100 hg38.150200.bed.split5592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5593 0 1 2 100 hg38.150200.bed.split5593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5594 0 1 2 100 hg38.150200.bed.split5594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5595 0 1 2 100 hg38.150200.bed.split5595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5596 0 1 2 100 hg38.150200.bed.split5596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5597 0 1 2 100 hg38.150200.bed.split5597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5598 0 1 2 100 hg38.150200.bed.split5598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5599 0 1 2 100 hg38.150200.bed.split5599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split56 0 1 2 100 hg38.150200.bed.split56.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split560 0 1 2 100 hg38.150200.bed.split560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5600 0 1 2 100 hg38.150200.bed.split5600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5601 0 1 2 100 hg38.150200.bed.split5601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5602 0 1 2 100 hg38.150200.bed.split5602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5603 0 1 2 100 hg38.150200.bed.split5603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5604 0 1 2 100 hg38.150200.bed.split5604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5605 0 1 2 100 hg38.150200.bed.split5605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5606 0 1 2 100 hg38.150200.bed.split5606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5607 0 1 2 100 hg38.150200.bed.split5607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5608 0 1 2 100 hg38.150200.bed.split5608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5609 0 1 2 100 hg38.150200.bed.split5609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split561 0 1 2 100 hg38.150200.bed.split561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5610 0 1 2 100 hg38.150200.bed.split5610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5611 0 1 2 100 hg38.150200.bed.split5611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5612 0 1 2 100 hg38.150200.bed.split5612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5613 0 1 2 100 hg38.150200.bed.split5613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5614 0 1 2 100 hg38.150200.bed.split5614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5615 0 1 2 100 hg38.150200.bed.split5615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5616 0 1 2 100 hg38.150200.bed.split5616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5617 0 1 2 100 hg38.150200.bed.split5617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5618 0 1 2 100 hg38.150200.bed.split5618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5619 0 1 2 100 hg38.150200.bed.split5619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split562 0 1 2 100 hg38.150200.bed.split562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5620 0 1 2 100 hg38.150200.bed.split5620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5621 0 1 2 100 hg38.150200.bed.split5621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5622 0 1 2 100 hg38.150200.bed.split5622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5623 0 1 2 100 hg38.150200.bed.split5623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5624 0 1 2 100 hg38.150200.bed.split5624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5625 0 1 2 100 hg38.150200.bed.split5625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5626 0 1 2 100 hg38.150200.bed.split5626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5627 0 1 2 100 hg38.150200.bed.split5627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5628 0 1 2 100 hg38.150200.bed.split5628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5629 0 1 2 100 hg38.150200.bed.split5629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split563 0 1 2 100 hg38.150200.bed.split563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5630 0 1 2 100 hg38.150200.bed.split5630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5631 0 1 2 100 hg38.150200.bed.split5631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5632 0 1 2 100 hg38.150200.bed.split5632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5633 0 1 2 100 hg38.150200.bed.split5633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5634 0 1 2 100 hg38.150200.bed.split5634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5635 0 1 2 100 hg38.150200.bed.split5635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5636 0 1 2 100 hg38.150200.bed.split5636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5637 0 1 2 100 hg38.150200.bed.split5637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5638 0 1 2 100 hg38.150200.bed.split5638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5639 0 1 2 100 hg38.150200.bed.split5639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split564 0 1 2 100 hg38.150200.bed.split564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5640 0 1 2 100 hg38.150200.bed.split5640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5641 0 1 2 100 hg38.150200.bed.split5641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5642 0 1 2 100 hg38.150200.bed.split5642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5643 0 1 2 100 hg38.150200.bed.split5643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5644 0 1 2 100 hg38.150200.bed.split5644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5645 0 1 2 100 hg38.150200.bed.split5645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5646 0 1 2 100 hg38.150200.bed.split5646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5647 0 1 2 100 hg38.150200.bed.split5647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5648 0 1 2 100 hg38.150200.bed.split5648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5649 0 1 2 100 hg38.150200.bed.split5649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split565 0 1 2 100 hg38.150200.bed.split565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5650 0 1 2 100 hg38.150200.bed.split5650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5651 0 1 2 100 hg38.150200.bed.split5651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5652 0 1 2 100 hg38.150200.bed.split5652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5653 0 1 2 100 hg38.150200.bed.split5653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5654 0 1 2 100 hg38.150200.bed.split5654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5655 0 1 2 100 hg38.150200.bed.split5655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5656 0 1 2 100 hg38.150200.bed.split5656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5657 0 1 2 100 hg38.150200.bed.split5657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5658 0 1 2 100 hg38.150200.bed.split5658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5659 0 1 2 100 hg38.150200.bed.split5659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split566 0 1 2 100 hg38.150200.bed.split566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5660 0 1 2 100 hg38.150200.bed.split5660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5661 0 1 2 100 hg38.150200.bed.split5661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5662 0 1 2 100 hg38.150200.bed.split5662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5663 0 1 2 100 hg38.150200.bed.split5663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5664 0 1 2 100 hg38.150200.bed.split5664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5665 0 1 2 100 hg38.150200.bed.split5665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5666 0 1 2 100 hg38.150200.bed.split5666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5667 0 1 2 100 hg38.150200.bed.split5667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5668 0 1 2 100 hg38.150200.bed.split5668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5669 0 1 2 100 hg38.150200.bed.split5669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split567 0 1 2 100 hg38.150200.bed.split567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5670 0 1 2 100 hg38.150200.bed.split5670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5671 0 1 2 100 hg38.150200.bed.split5671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5672 0 1 2 100 hg38.150200.bed.split5672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5673 0 1 2 100 hg38.150200.bed.split5673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5674 0 1 2 100 hg38.150200.bed.split5674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5675 0 1 2 100 hg38.150200.bed.split5675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5676 0 1 2 100 hg38.150200.bed.split5676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5677 0 1 2 100 hg38.150200.bed.split5677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5678 0 1 2 100 hg38.150200.bed.split5678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5679 0 1 2 100 hg38.150200.bed.split5679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split568 0 1 2 100 hg38.150200.bed.split568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5680 0 1 2 100 hg38.150200.bed.split5680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5681 0 1 2 100 hg38.150200.bed.split5681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5682 0 1 2 100 hg38.150200.bed.split5682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5683 0 1 2 100 hg38.150200.bed.split5683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5684 0 1 2 100 hg38.150200.bed.split5684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5685 0 1 2 100 hg38.150200.bed.split5685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5686 0 1 2 100 hg38.150200.bed.split5686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5687 0 1 2 100 hg38.150200.bed.split5687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5688 0 1 2 100 hg38.150200.bed.split5688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5689 0 1 2 100 hg38.150200.bed.split5689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split569 0 1 2 100 hg38.150200.bed.split569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5690 0 1 2 100 hg38.150200.bed.split5690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5691 0 1 2 100 hg38.150200.bed.split5691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5692 0 1 2 100 hg38.150200.bed.split5692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5693 0 1 2 100 hg38.150200.bed.split5693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5694 0 1 2 100 hg38.150200.bed.split5694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5695 0 1 2 100 hg38.150200.bed.split5695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5696 0 1 2 100 hg38.150200.bed.split5696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5697 0 1 2 100 hg38.150200.bed.split5697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5698 0 1 2 100 hg38.150200.bed.split5698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5699 0 1 2 100 hg38.150200.bed.split5699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split57 0 1 2 100 hg38.150200.bed.split57.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split570 0 1 2 100 hg38.150200.bed.split570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5700 0 1 2 100 hg38.150200.bed.split5700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5701 0 1 2 100 hg38.150200.bed.split5701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5702 0 1 2 100 hg38.150200.bed.split5702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5703 0 1 2 100 hg38.150200.bed.split5703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5704 0 1 2 100 hg38.150200.bed.split5704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5705 0 1 2 100 hg38.150200.bed.split5705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5706 0 1 2 100 hg38.150200.bed.split5706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5707 0 1 2 100 hg38.150200.bed.split5707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5708 0 1 2 100 hg38.150200.bed.split5708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5709 0 1 2 100 hg38.150200.bed.split5709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split571 0 1 2 100 hg38.150200.bed.split571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5710 0 1 2 100 hg38.150200.bed.split5710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5711 0 1 2 100 hg38.150200.bed.split5711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5712 0 1 2 100 hg38.150200.bed.split5712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5713 0 1 2 100 hg38.150200.bed.split5713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5714 0 1 2 100 hg38.150200.bed.split5714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5715 0 1 2 100 hg38.150200.bed.split5715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5716 0 1 2 100 hg38.150200.bed.split5716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5717 0 1 2 100 hg38.150200.bed.split5717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5718 0 1 2 100 hg38.150200.bed.split5718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5719 0 1 2 100 hg38.150200.bed.split5719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split572 0 1 2 100 hg38.150200.bed.split572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5720 0 1 2 100 hg38.150200.bed.split5720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5721 0 1 2 100 hg38.150200.bed.split5721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5722 0 1 2 100 hg38.150200.bed.split5722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5723 0 1 2 100 hg38.150200.bed.split5723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5724 0 1 2 100 hg38.150200.bed.split5724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5725 0 1 2 100 hg38.150200.bed.split5725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5726 0 1 2 100 hg38.150200.bed.split5726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5727 0 1 2 100 hg38.150200.bed.split5727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5728 0 1 2 100 hg38.150200.bed.split5728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5729 0 1 2 100 hg38.150200.bed.split5729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split573 0 1 2 100 hg38.150200.bed.split573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5730 0 1 2 100 hg38.150200.bed.split5730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5731 0 1 2 100 hg38.150200.bed.split5731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5732 0 1 2 100 hg38.150200.bed.split5732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5733 0 1 2 100 hg38.150200.bed.split5733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5734 0 1 2 100 hg38.150200.bed.split5734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5735 0 1 2 100 hg38.150200.bed.split5735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5736 0 1 2 100 hg38.150200.bed.split5736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5737 0 1 2 100 hg38.150200.bed.split5737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5738 0 1 2 100 hg38.150200.bed.split5738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5739 0 1 2 100 hg38.150200.bed.split5739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split574 0 1 2 100 hg38.150200.bed.split574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5740 0 1 2 100 hg38.150200.bed.split5740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5741 0 1 2 100 hg38.150200.bed.split5741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5742 0 1 2 100 hg38.150200.bed.split5742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5743 0 1 2 100 hg38.150200.bed.split5743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5744 0 1 2 100 hg38.150200.bed.split5744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5745 0 1 2 100 hg38.150200.bed.split5745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5746 0 1 2 100 hg38.150200.bed.split5746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5747 0 1 2 100 hg38.150200.bed.split5747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5748 0 1 2 100 hg38.150200.bed.split5748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5749 0 1 2 100 hg38.150200.bed.split5749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split575 0 1 2 100 hg38.150200.bed.split575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5750 0 1 2 100 hg38.150200.bed.split5750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5751 0 1 2 100 hg38.150200.bed.split5751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5752 0 1 2 100 hg38.150200.bed.split5752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5753 0 1 2 100 hg38.150200.bed.split5753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5754 0 1 2 100 hg38.150200.bed.split5754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5755 0 1 2 100 hg38.150200.bed.split5755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5756 0 1 2 100 hg38.150200.bed.split5756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5757 0 1 2 100 hg38.150200.bed.split5757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5758 0 1 2 100 hg38.150200.bed.split5758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5759 0 1 2 100 hg38.150200.bed.split5759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split576 0 1 2 100 hg38.150200.bed.split576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5760 0 1 2 100 hg38.150200.bed.split5760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5761 0 1 2 100 hg38.150200.bed.split5761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5762 0 1 2 100 hg38.150200.bed.split5762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5763 0 1 2 100 hg38.150200.bed.split5763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5764 0 1 2 100 hg38.150200.bed.split5764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5765 0 1 2 100 hg38.150200.bed.split5765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5766 0 1 2 100 hg38.150200.bed.split5766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5767 0 1 2 100 hg38.150200.bed.split5767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5768 0 1 2 100 hg38.150200.bed.split5768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5769 0 1 2 100 hg38.150200.bed.split5769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split577 0 1 2 100 hg38.150200.bed.split577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5770 0 1 2 100 hg38.150200.bed.split5770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5771 0 1 2 100 hg38.150200.bed.split5771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5772 0 1 2 100 hg38.150200.bed.split5772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5773 0 1 2 100 hg38.150200.bed.split5773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5774 0 1 2 100 hg38.150200.bed.split5774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5775 0 1 2 100 hg38.150200.bed.split5775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5776 0 1 2 100 hg38.150200.bed.split5776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5777 0 1 2 100 hg38.150200.bed.split5777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5778 0 1 2 100 hg38.150200.bed.split5778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5779 0 1 2 100 hg38.150200.bed.split5779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split578 0 1 2 100 hg38.150200.bed.split578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5780 0 1 2 100 hg38.150200.bed.split5780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5781 0 1 2 100 hg38.150200.bed.split5781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5782 0 1 2 100 hg38.150200.bed.split5782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5783 0 1 2 100 hg38.150200.bed.split5783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5784 0 1 2 100 hg38.150200.bed.split5784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5785 0 1 2 100 hg38.150200.bed.split5785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5786 0 1 2 100 hg38.150200.bed.split5786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5787 0 1 2 100 hg38.150200.bed.split5787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5788 0 1 2 100 hg38.150200.bed.split5788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5789 0 1 2 100 hg38.150200.bed.split5789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split579 0 1 2 100 hg38.150200.bed.split579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5790 0 1 2 100 hg38.150200.bed.split5790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5791 0 1 2 100 hg38.150200.bed.split5791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5792 0 1 2 100 hg38.150200.bed.split5792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5793 0 1 2 100 hg38.150200.bed.split5793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5794 0 1 2 100 hg38.150200.bed.split5794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5795 0 1 2 100 hg38.150200.bed.split5795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5796 0 1 2 100 hg38.150200.bed.split5796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5797 0 1 2 100 hg38.150200.bed.split5797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5798 0 1 2 100 hg38.150200.bed.split5798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5799 0 1 2 100 hg38.150200.bed.split5799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split58 0 1 2 100 hg38.150200.bed.split58.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split580 0 1 2 100 hg38.150200.bed.split580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5800 0 1 2 100 hg38.150200.bed.split5800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5801 0 1 2 100 hg38.150200.bed.split5801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5802 0 1 2 100 hg38.150200.bed.split5802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5803 0 1 2 100 hg38.150200.bed.split5803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5804 0 1 2 100 hg38.150200.bed.split5804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5805 0 1 2 100 hg38.150200.bed.split5805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5806 0 1 2 100 hg38.150200.bed.split5806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5807 0 1 2 100 hg38.150200.bed.split5807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5808 0 1 2 100 hg38.150200.bed.split5808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5809 0 1 2 100 hg38.150200.bed.split5809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split581 0 1 2 100 hg38.150200.bed.split581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5810 0 1 2 100 hg38.150200.bed.split5810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5811 0 1 2 100 hg38.150200.bed.split5811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5812 0 1 2 100 hg38.150200.bed.split5812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5813 0 1 2 100 hg38.150200.bed.split5813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5814 0 1 2 100 hg38.150200.bed.split5814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5815 0 1 2 100 hg38.150200.bed.split5815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5816 0 1 2 100 hg38.150200.bed.split5816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5817 0 1 2 100 hg38.150200.bed.split5817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5818 0 1 2 100 hg38.150200.bed.split5818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5819 0 1 2 100 hg38.150200.bed.split5819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split582 0 1 2 100 hg38.150200.bed.split582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5820 0 1 2 100 hg38.150200.bed.split5820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5821 0 1 2 100 hg38.150200.bed.split5821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5822 0 1 2 100 hg38.150200.bed.split5822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5823 0 1 2 100 hg38.150200.bed.split5823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5824 0 1 2 100 hg38.150200.bed.split5824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5825 0 1 2 100 hg38.150200.bed.split5825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5826 0 1 2 100 hg38.150200.bed.split5826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5827 0 1 2 100 hg38.150200.bed.split5827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5828 0 1 2 100 hg38.150200.bed.split5828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5829 0 1 2 100 hg38.150200.bed.split5829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split583 0 1 2 100 hg38.150200.bed.split583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5830 0 1 2 100 hg38.150200.bed.split5830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5831 0 1 2 100 hg38.150200.bed.split5831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5832 0 1 2 100 hg38.150200.bed.split5832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5833 0 1 2 100 hg38.150200.bed.split5833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5834 0 1 2 100 hg38.150200.bed.split5834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5835 0 1 2 100 hg38.150200.bed.split5835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5836 0 1 2 100 hg38.150200.bed.split5836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5837 0 1 2 100 hg38.150200.bed.split5837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5838 0 1 2 100 hg38.150200.bed.split5838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5839 0 1 2 100 hg38.150200.bed.split5839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split584 0 1 2 100 hg38.150200.bed.split584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5840 0 1 2 100 hg38.150200.bed.split5840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5841 0 1 2 100 hg38.150200.bed.split5841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5842 0 1 2 100 hg38.150200.bed.split5842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5843 0 1 2 100 hg38.150200.bed.split5843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5844 0 1 2 100 hg38.150200.bed.split5844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5845 0 1 2 100 hg38.150200.bed.split5845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5846 0 1 2 100 hg38.150200.bed.split5846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5847 0 1 2 100 hg38.150200.bed.split5847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5848 0 1 2 100 hg38.150200.bed.split5848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5849 0 1 2 100 hg38.150200.bed.split5849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split585 0 1 2 100 hg38.150200.bed.split585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5850 0 1 2 100 hg38.150200.bed.split5850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5851 0 1 2 100 hg38.150200.bed.split5851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5852 0 1 2 100 hg38.150200.bed.split5852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5853 0 1 2 100 hg38.150200.bed.split5853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5854 0 1 2 100 hg38.150200.bed.split5854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5855 0 1 2 100 hg38.150200.bed.split5855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5856 0 1 2 100 hg38.150200.bed.split5856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5857 0 1 2 100 hg38.150200.bed.split5857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5858 0 1 2 100 hg38.150200.bed.split5858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5859 0 1 2 100 hg38.150200.bed.split5859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split586 0 1 2 100 hg38.150200.bed.split586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5860 0 1 2 100 hg38.150200.bed.split5860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5861 0 1 2 100 hg38.150200.bed.split5861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5862 0 1 2 100 hg38.150200.bed.split5862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5863 0 1 2 100 hg38.150200.bed.split5863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5864 0 1 2 100 hg38.150200.bed.split5864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5865 0 1 2 100 hg38.150200.bed.split5865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5866 0 1 2 100 hg38.150200.bed.split5866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5867 0 1 2 100 hg38.150200.bed.split5867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5868 0 1 2 100 hg38.150200.bed.split5868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5869 0 1 2 100 hg38.150200.bed.split5869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split587 0 1 2 100 hg38.150200.bed.split587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5870 0 1 2 100 hg38.150200.bed.split5870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5871 0 1 2 100 hg38.150200.bed.split5871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5872 0 1 2 100 hg38.150200.bed.split5872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5873 0 1 2 100 hg38.150200.bed.split5873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5874 0 1 2 100 hg38.150200.bed.split5874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5875 0 1 2 100 hg38.150200.bed.split5875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5876 0 1 2 100 hg38.150200.bed.split5876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5877 0 1 2 100 hg38.150200.bed.split5877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5878 0 1 2 100 hg38.150200.bed.split5878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5879 0 1 2 100 hg38.150200.bed.split5879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split588 0 1 2 100 hg38.150200.bed.split588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5880 0 1 2 100 hg38.150200.bed.split5880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5881 0 1 2 100 hg38.150200.bed.split5881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5882 0 1 2 100 hg38.150200.bed.split5882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5883 0 1 2 100 hg38.150200.bed.split5883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5884 0 1 2 100 hg38.150200.bed.split5884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5885 0 1 2 100 hg38.150200.bed.split5885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5886 0 1 2 100 hg38.150200.bed.split5886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5887 0 1 2 100 hg38.150200.bed.split5887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5888 0 1 2 100 hg38.150200.bed.split5888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5889 0 1 2 100 hg38.150200.bed.split5889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split589 0 1 2 100 hg38.150200.bed.split589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5890 0 1 2 100 hg38.150200.bed.split5890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5891 0 1 2 100 hg38.150200.bed.split5891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5892 0 1 2 100 hg38.150200.bed.split5892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5893 0 1 2 100 hg38.150200.bed.split5893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5894 0 1 2 100 hg38.150200.bed.split5894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5895 0 1 2 100 hg38.150200.bed.split5895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5896 0 1 2 100 hg38.150200.bed.split5896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5897 0 1 2 100 hg38.150200.bed.split5897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5898 0 1 2 100 hg38.150200.bed.split5898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5899 0 1 2 100 hg38.150200.bed.split5899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split59 0 1 2 100 hg38.150200.bed.split59.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split590 0 1 2 100 hg38.150200.bed.split590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5900 0 1 2 100 hg38.150200.bed.split5900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5901 0 1 2 100 hg38.150200.bed.split5901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5902 0 1 2 100 hg38.150200.bed.split5902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5903 0 1 2 100 hg38.150200.bed.split5903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5904 0 1 2 100 hg38.150200.bed.split5904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5905 0 1 2 100 hg38.150200.bed.split5905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5906 0 1 2 100 hg38.150200.bed.split5906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5907 0 1 2 100 hg38.150200.bed.split5907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5908 0 1 2 100 hg38.150200.bed.split5908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5909 0 1 2 100 hg38.150200.bed.split5909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split591 0 1 2 100 hg38.150200.bed.split591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5910 0 1 2 100 hg38.150200.bed.split5910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5911 0 1 2 100 hg38.150200.bed.split5911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5912 0 1 2 100 hg38.150200.bed.split5912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5913 0 1 2 100 hg38.150200.bed.split5913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5914 0 1 2 100 hg38.150200.bed.split5914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5915 0 1 2 100 hg38.150200.bed.split5915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5916 0 1 2 100 hg38.150200.bed.split5916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5917 0 1 2 100 hg38.150200.bed.split5917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5918 0 1 2 100 hg38.150200.bed.split5918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5919 0 1 2 100 hg38.150200.bed.split5919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split592 0 1 2 100 hg38.150200.bed.split592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5920 0 1 2 100 hg38.150200.bed.split5920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5921 0 1 2 100 hg38.150200.bed.split5921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5922 0 1 2 100 hg38.150200.bed.split5922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5923 0 1 2 100 hg38.150200.bed.split5923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5924 0 1 2 100 hg38.150200.bed.split5924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5925 0 1 2 100 hg38.150200.bed.split5925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5926 0 1 2 100 hg38.150200.bed.split5926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5927 0 1 2 100 hg38.150200.bed.split5927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5928 0 1 2 100 hg38.150200.bed.split5928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5929 0 1 2 100 hg38.150200.bed.split5929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split593 0 1 2 100 hg38.150200.bed.split593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5930 0 1 2 100 hg38.150200.bed.split5930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5931 0 1 2 100 hg38.150200.bed.split5931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5932 0 1 2 100 hg38.150200.bed.split5932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5933 0 1 2 100 hg38.150200.bed.split5933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5934 0 1 2 100 hg38.150200.bed.split5934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5935 0 1 2 100 hg38.150200.bed.split5935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5936 0 1 2 100 hg38.150200.bed.split5936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5937 0 1 2 100 hg38.150200.bed.split5937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5938 0 1 2 100 hg38.150200.bed.split5938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5939 0 1 2 100 hg38.150200.bed.split5939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split594 0 1 2 100 hg38.150200.bed.split594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5940 0 1 2 100 hg38.150200.bed.split5940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5941 0 1 2 100 hg38.150200.bed.split5941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5942 0 1 2 100 hg38.150200.bed.split5942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5943 0 1 2 100 hg38.150200.bed.split5943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5944 0 1 2 100 hg38.150200.bed.split5944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5945 0 1 2 100 hg38.150200.bed.split5945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5946 0 1 2 100 hg38.150200.bed.split5946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5947 0 1 2 100 hg38.150200.bed.split5947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5948 0 1 2 100 hg38.150200.bed.split5948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5949 0 1 2 100 hg38.150200.bed.split5949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split595 0 1 2 100 hg38.150200.bed.split595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5950 0 1 2 100 hg38.150200.bed.split5950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5951 0 1 2 100 hg38.150200.bed.split5951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5952 0 1 2 100 hg38.150200.bed.split5952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5953 0 1 2 100 hg38.150200.bed.split5953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5954 0 1 2 100 hg38.150200.bed.split5954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5955 0 1 2 100 hg38.150200.bed.split5955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5956 0 1 2 100 hg38.150200.bed.split5956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5957 0 1 2 100 hg38.150200.bed.split5957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5958 0 1 2 100 hg38.150200.bed.split5958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5959 0 1 2 100 hg38.150200.bed.split5959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split596 0 1 2 100 hg38.150200.bed.split596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5960 0 1 2 100 hg38.150200.bed.split5960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5961 0 1 2 100 hg38.150200.bed.split5961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5962 0 1 2 100 hg38.150200.bed.split5962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5963 0 1 2 100 hg38.150200.bed.split5963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5964 0 1 2 100 hg38.150200.bed.split5964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5965 0 1 2 100 hg38.150200.bed.split5965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5966 0 1 2 100 hg38.150200.bed.split5966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5967 0 1 2 100 hg38.150200.bed.split5967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5968 0 1 2 100 hg38.150200.bed.split5968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5969 0 1 2 100 hg38.150200.bed.split5969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split597 0 1 2 100 hg38.150200.bed.split597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5970 0 1 2 100 hg38.150200.bed.split5970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5971 0 1 2 100 hg38.150200.bed.split5971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5972 0 1 2 100 hg38.150200.bed.split5972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5973 0 1 2 100 hg38.150200.bed.split5973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5974 0 1 2 100 hg38.150200.bed.split5974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5975 0 1 2 100 hg38.150200.bed.split5975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5976 0 1 2 100 hg38.150200.bed.split5976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5977 0 1 2 100 hg38.150200.bed.split5977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5978 0 1 2 100 hg38.150200.bed.split5978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5979 0 1 2 100 hg38.150200.bed.split5979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split598 0 1 2 100 hg38.150200.bed.split598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5980 0 1 2 100 hg38.150200.bed.split5980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5981 0 1 2 100 hg38.150200.bed.split5981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5982 0 1 2 100 hg38.150200.bed.split5982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5983 0 1 2 100 hg38.150200.bed.split5983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5984 0 1 2 100 hg38.150200.bed.split5984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5985 0 1 2 100 hg38.150200.bed.split5985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5986 0 1 2 100 hg38.150200.bed.split5986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5987 0 1 2 100 hg38.150200.bed.split5987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5988 0 1 2 100 hg38.150200.bed.split5988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5989 0 1 2 100 hg38.150200.bed.split5989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split599 0 1 2 100 hg38.150200.bed.split599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5990 0 1 2 100 hg38.150200.bed.split5990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5991 0 1 2 100 hg38.150200.bed.split5991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5992 0 1 2 100 hg38.150200.bed.split5992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5993 0 1 2 100 hg38.150200.bed.split5993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5994 0 1 2 100 hg38.150200.bed.split5994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5995 0 1 2 100 hg38.150200.bed.split5995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5996 0 1 2 100 hg38.150200.bed.split5996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5997 0 1 2 100 hg38.150200.bed.split5997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5998 0 1 2 100 hg38.150200.bed.split5998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split5999 0 1 2 100 hg38.150200.bed.split5999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6 0 1 2 100 hg38.150200.bed.split6.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split60 0 1 2 100 hg38.150200.bed.split60.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split600 0 1 2 100 hg38.150200.bed.split600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6000 0 1 2 100 hg38.150200.bed.split6000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6001 0 1 2 100 hg38.150200.bed.split6001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6002 0 1 2 100 hg38.150200.bed.split6002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6003 0 1 2 100 hg38.150200.bed.split6003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6004 0 1 2 100 hg38.150200.bed.split6004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6005 0 1 2 100 hg38.150200.bed.split6005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6006 0 1 2 100 hg38.150200.bed.split6006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6007 0 1 2 100 hg38.150200.bed.split6007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6008 0 1 2 100 hg38.150200.bed.split6008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6009 0 1 2 100 hg38.150200.bed.split6009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split601 0 1 2 100 hg38.150200.bed.split601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6010 0 1 2 100 hg38.150200.bed.split6010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6011 0 1 2 100 hg38.150200.bed.split6011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6012 0 1 2 100 hg38.150200.bed.split6012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6013 0 1 2 100 hg38.150200.bed.split6013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6014 0 1 2 100 hg38.150200.bed.split6014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6015 0 1 2 100 hg38.150200.bed.split6015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6016 0 1 2 100 hg38.150200.bed.split6016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6017 0 1 2 100 hg38.150200.bed.split6017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6018 0 1 2 100 hg38.150200.bed.split6018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6019 0 1 2 100 hg38.150200.bed.split6019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split602 0 1 2 100 hg38.150200.bed.split602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6020 0 1 2 100 hg38.150200.bed.split6020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6021 0 1 2 100 hg38.150200.bed.split6021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6022 0 1 2 100 hg38.150200.bed.split6022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6023 0 1 2 100 hg38.150200.bed.split6023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6024 0 1 2 100 hg38.150200.bed.split6024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6025 0 1 2 100 hg38.150200.bed.split6025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6026 0 1 2 100 hg38.150200.bed.split6026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6027 0 1 2 100 hg38.150200.bed.split6027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6028 0 1 2 100 hg38.150200.bed.split6028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6029 0 1 2 100 hg38.150200.bed.split6029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split603 0 1 2 100 hg38.150200.bed.split603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6030 0 1 2 100 hg38.150200.bed.split6030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6031 0 1 2 100 hg38.150200.bed.split6031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6032 0 1 2 100 hg38.150200.bed.split6032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6033 0 1 2 100 hg38.150200.bed.split6033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6034 0 1 2 100 hg38.150200.bed.split6034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6035 0 1 2 100 hg38.150200.bed.split6035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6036 0 1 2 100 hg38.150200.bed.split6036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6037 0 1 2 100 hg38.150200.bed.split6037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6038 0 1 2 100 hg38.150200.bed.split6038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6039 0 1 2 100 hg38.150200.bed.split6039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split604 0 1 2 100 hg38.150200.bed.split604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6040 0 1 2 100 hg38.150200.bed.split6040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6041 0 1 2 100 hg38.150200.bed.split6041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6042 0 1 2 100 hg38.150200.bed.split6042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6043 0 1 2 100 hg38.150200.bed.split6043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6044 0 1 2 100 hg38.150200.bed.split6044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6045 0 1 2 100 hg38.150200.bed.split6045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6046 0 1 2 100 hg38.150200.bed.split6046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6047 0 1 2 100 hg38.150200.bed.split6047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6048 0 1 2 100 hg38.150200.bed.split6048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6049 0 1 2 100 hg38.150200.bed.split6049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split605 0 1 2 100 hg38.150200.bed.split605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6050 0 1 2 100 hg38.150200.bed.split6050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6051 0 1 2 100 hg38.150200.bed.split6051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6052 0 1 2 100 hg38.150200.bed.split6052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6053 0 1 2 100 hg38.150200.bed.split6053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6054 0 1 2 100 hg38.150200.bed.split6054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6055 0 1 2 100 hg38.150200.bed.split6055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6056 0 1 2 100 hg38.150200.bed.split6056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6057 0 1 2 100 hg38.150200.bed.split6057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6058 0 1 2 100 hg38.150200.bed.split6058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6059 0 1 2 100 hg38.150200.bed.split6059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split606 0 1 2 100 hg38.150200.bed.split606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6060 0 1 2 100 hg38.150200.bed.split6060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6061 0 1 2 100 hg38.150200.bed.split6061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6062 0 1 2 100 hg38.150200.bed.split6062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6063 0 1 2 100 hg38.150200.bed.split6063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6064 0 1 2 100 hg38.150200.bed.split6064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6065 0 1 2 100 hg38.150200.bed.split6065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6066 0 1 2 100 hg38.150200.bed.split6066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6067 0 1 2 100 hg38.150200.bed.split6067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6068 0 1 2 100 hg38.150200.bed.split6068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6069 0 1 2 100 hg38.150200.bed.split6069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split607 0 1 2 100 hg38.150200.bed.split607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6070 0 1 2 100 hg38.150200.bed.split6070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6071 0 1 2 100 hg38.150200.bed.split6071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6072 0 1 2 100 hg38.150200.bed.split6072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6073 0 1 2 100 hg38.150200.bed.split6073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6074 0 1 2 100 hg38.150200.bed.split6074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6075 0 1 2 100 hg38.150200.bed.split6075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6076 0 1 2 100 hg38.150200.bed.split6076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6077 0 1 2 100 hg38.150200.bed.split6077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6078 0 1 2 100 hg38.150200.bed.split6078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6079 0 1 2 100 hg38.150200.bed.split6079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split608 0 1 2 100 hg38.150200.bed.split608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6080 0 1 2 100 hg38.150200.bed.split6080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6081 0 1 2 100 hg38.150200.bed.split6081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6082 0 1 2 100 hg38.150200.bed.split6082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6083 0 1 2 100 hg38.150200.bed.split6083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6084 0 1 2 100 hg38.150200.bed.split6084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6085 0 1 2 100 hg38.150200.bed.split6085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6086 0 1 2 100 hg38.150200.bed.split6086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6087 0 1 2 100 hg38.150200.bed.split6087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6088 0 1 2 100 hg38.150200.bed.split6088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6089 0 1 2 100 hg38.150200.bed.split6089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split609 0 1 2 100 hg38.150200.bed.split609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6090 0 1 2 100 hg38.150200.bed.split6090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6091 0 1 2 100 hg38.150200.bed.split6091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6092 0 1 2 100 hg38.150200.bed.split6092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6093 0 1 2 100 hg38.150200.bed.split6093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6094 0 1 2 100 hg38.150200.bed.split6094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6095 0 1 2 100 hg38.150200.bed.split6095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6096 0 1 2 100 hg38.150200.bed.split6096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6097 0 1 2 100 hg38.150200.bed.split6097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6098 0 1 2 100 hg38.150200.bed.split6098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6099 0 1 2 100 hg38.150200.bed.split6099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split61 0 1 2 100 hg38.150200.bed.split61.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split610 0 1 2 100 hg38.150200.bed.split610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6100 0 1 2 100 hg38.150200.bed.split6100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6101 0 1 2 100 hg38.150200.bed.split6101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6102 0 1 2 100 hg38.150200.bed.split6102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6103 0 1 2 100 hg38.150200.bed.split6103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6104 0 1 2 100 hg38.150200.bed.split6104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6105 0 1 2 100 hg38.150200.bed.split6105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6106 0 1 2 100 hg38.150200.bed.split6106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6107 0 1 2 100 hg38.150200.bed.split6107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6108 0 1 2 100 hg38.150200.bed.split6108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6109 0 1 2 100 hg38.150200.bed.split6109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split611 0 1 2 100 hg38.150200.bed.split611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6110 0 1 2 100 hg38.150200.bed.split6110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6111 0 1 2 100 hg38.150200.bed.split6111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6112 0 1 2 100 hg38.150200.bed.split6112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6113 0 1 2 100 hg38.150200.bed.split6113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6114 0 1 2 100 hg38.150200.bed.split6114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6115 0 1 2 100 hg38.150200.bed.split6115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6116 0 1 2 100 hg38.150200.bed.split6116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6117 0 1 2 100 hg38.150200.bed.split6117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6118 0 1 2 100 hg38.150200.bed.split6118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6119 0 1 2 100 hg38.150200.bed.split6119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split612 0 1 2 100 hg38.150200.bed.split612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6120 0 1 2 100 hg38.150200.bed.split6120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6121 0 1 2 100 hg38.150200.bed.split6121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6122 0 1 2 100 hg38.150200.bed.split6122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6123 0 1 2 100 hg38.150200.bed.split6123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6124 0 1 2 100 hg38.150200.bed.split6124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6125 0 1 2 100 hg38.150200.bed.split6125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6126 0 1 2 100 hg38.150200.bed.split6126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6127 0 1 2 100 hg38.150200.bed.split6127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6128 0 1 2 100 hg38.150200.bed.split6128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6129 0 1 2 100 hg38.150200.bed.split6129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split613 0 1 2 100 hg38.150200.bed.split613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6130 0 1 2 100 hg38.150200.bed.split6130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6131 0 1 2 100 hg38.150200.bed.split6131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6132 0 1 2 100 hg38.150200.bed.split6132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6133 0 1 2 100 hg38.150200.bed.split6133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6134 0 1 2 100 hg38.150200.bed.split6134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6135 0 1 2 100 hg38.150200.bed.split6135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6136 0 1 2 100 hg38.150200.bed.split6136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6137 0 1 2 100 hg38.150200.bed.split6137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6138 0 1 2 100 hg38.150200.bed.split6138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6139 0 1 2 100 hg38.150200.bed.split6139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split614 0 1 2 100 hg38.150200.bed.split614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6140 0 1 2 100 hg38.150200.bed.split6140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6141 0 1 2 100 hg38.150200.bed.split6141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6142 0 1 2 100 hg38.150200.bed.split6142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6143 0 1 2 100 hg38.150200.bed.split6143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6144 0 1 2 100 hg38.150200.bed.split6144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6145 0 1 2 100 hg38.150200.bed.split6145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6146 0 1 2 100 hg38.150200.bed.split6146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6147 0 1 2 100 hg38.150200.bed.split6147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6148 0 1 2 100 hg38.150200.bed.split6148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6149 0 1 2 100 hg38.150200.bed.split6149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split615 0 1 2 100 hg38.150200.bed.split615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6150 0 1 2 100 hg38.150200.bed.split6150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6151 0 1 2 100 hg38.150200.bed.split6151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6152 0 1 2 100 hg38.150200.bed.split6152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6153 0 1 2 100 hg38.150200.bed.split6153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6154 0 1 2 100 hg38.150200.bed.split6154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6155 0 1 2 100 hg38.150200.bed.split6155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6156 0 1 2 100 hg38.150200.bed.split6156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6157 0 1 2 100 hg38.150200.bed.split6157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6158 0 1 2 100 hg38.150200.bed.split6158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6159 0 1 2 100 hg38.150200.bed.split6159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split616 0 1 2 100 hg38.150200.bed.split616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6160 0 1 2 100 hg38.150200.bed.split6160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6161 0 1 2 100 hg38.150200.bed.split6161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6162 0 1 2 100 hg38.150200.bed.split6162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6163 0 1 2 100 hg38.150200.bed.split6163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6164 0 1 2 100 hg38.150200.bed.split6164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6165 0 1 2 100 hg38.150200.bed.split6165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6166 0 1 2 100 hg38.150200.bed.split6166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6167 0 1 2 100 hg38.150200.bed.split6167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6168 0 1 2 100 hg38.150200.bed.split6168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6169 0 1 2 100 hg38.150200.bed.split6169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split617 0 1 2 100 hg38.150200.bed.split617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6170 0 1 2 100 hg38.150200.bed.split6170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6171 0 1 2 100 hg38.150200.bed.split6171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6172 0 1 2 100 hg38.150200.bed.split6172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6173 0 1 2 100 hg38.150200.bed.split6173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6174 0 1 2 100 hg38.150200.bed.split6174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6175 0 1 2 100 hg38.150200.bed.split6175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6176 0 1 2 100 hg38.150200.bed.split6176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6177 0 1 2 100 hg38.150200.bed.split6177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6178 0 1 2 100 hg38.150200.bed.split6178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6179 0 1 2 100 hg38.150200.bed.split6179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split618 0 1 2 100 hg38.150200.bed.split618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6180 0 1 2 100 hg38.150200.bed.split6180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6181 0 1 2 100 hg38.150200.bed.split6181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6182 0 1 2 100 hg38.150200.bed.split6182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6183 0 1 2 100 hg38.150200.bed.split6183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6184 0 1 2 100 hg38.150200.bed.split6184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6185 0 1 2 100 hg38.150200.bed.split6185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6186 0 1 2 100 hg38.150200.bed.split6186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6187 0 1 2 100 hg38.150200.bed.split6187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6188 0 1 2 100 hg38.150200.bed.split6188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6189 0 1 2 100 hg38.150200.bed.split6189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split619 0 1 2 100 hg38.150200.bed.split619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6190 0 1 2 100 hg38.150200.bed.split6190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6191 0 1 2 100 hg38.150200.bed.split6191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6192 0 1 2 100 hg38.150200.bed.split6192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6193 0 1 2 100 hg38.150200.bed.split6193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6194 0 1 2 100 hg38.150200.bed.split6194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6195 0 1 2 100 hg38.150200.bed.split6195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6196 0 1 2 100 hg38.150200.bed.split6196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6197 0 1 2 100 hg38.150200.bed.split6197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6198 0 1 2 100 hg38.150200.bed.split6198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6199 0 1 2 100 hg38.150200.bed.split6199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split62 0 1 2 100 hg38.150200.bed.split62.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split620 0 1 2 100 hg38.150200.bed.split620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6200 0 1 2 100 hg38.150200.bed.split6200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6201 0 1 2 100 hg38.150200.bed.split6201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6202 0 1 2 100 hg38.150200.bed.split6202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6203 0 1 2 100 hg38.150200.bed.split6203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6204 0 1 2 100 hg38.150200.bed.split6204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6205 0 1 2 100 hg38.150200.bed.split6205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6206 0 1 2 100 hg38.150200.bed.split6206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6207 0 1 2 100 hg38.150200.bed.split6207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6208 0 1 2 100 hg38.150200.bed.split6208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6209 0 1 2 100 hg38.150200.bed.split6209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split621 0 1 2 100 hg38.150200.bed.split621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6210 0 1 2 100 hg38.150200.bed.split6210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6211 0 1 2 100 hg38.150200.bed.split6211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6212 0 1 2 100 hg38.150200.bed.split6212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6213 0 1 2 100 hg38.150200.bed.split6213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6214 0 1 2 100 hg38.150200.bed.split6214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6215 0 1 2 100 hg38.150200.bed.split6215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6216 0 1 2 100 hg38.150200.bed.split6216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6217 0 1 2 100 hg38.150200.bed.split6217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6218 0 1 2 100 hg38.150200.bed.split6218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6219 0 1 2 100 hg38.150200.bed.split6219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split622 0 1 2 100 hg38.150200.bed.split622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6220 0 1 2 100 hg38.150200.bed.split6220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6221 0 1 2 100 hg38.150200.bed.split6221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6222 0 1 2 100 hg38.150200.bed.split6222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6223 0 1 2 100 hg38.150200.bed.split6223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6224 0 1 2 100 hg38.150200.bed.split6224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6225 0 1 2 100 hg38.150200.bed.split6225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6226 0 1 2 100 hg38.150200.bed.split6226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6227 0 1 2 100 hg38.150200.bed.split6227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6228 0 1 2 100 hg38.150200.bed.split6228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6229 0 1 2 100 hg38.150200.bed.split6229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split623 0 1 2 100 hg38.150200.bed.split623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6230 0 1 2 100 hg38.150200.bed.split6230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6231 0 1 2 100 hg38.150200.bed.split6231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6232 0 1 2 100 hg38.150200.bed.split6232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6233 0 1 2 100 hg38.150200.bed.split6233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6234 0 1 2 100 hg38.150200.bed.split6234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6235 0 1 2 100 hg38.150200.bed.split6235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6236 0 1 2 100 hg38.150200.bed.split6236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6237 0 1 2 100 hg38.150200.bed.split6237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6238 0 1 2 100 hg38.150200.bed.split6238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6239 0 1 2 100 hg38.150200.bed.split6239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split624 0 1 2 100 hg38.150200.bed.split624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6240 0 1 2 100 hg38.150200.bed.split6240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6241 0 1 2 100 hg38.150200.bed.split6241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6242 0 1 2 100 hg38.150200.bed.split6242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6243 0 1 2 100 hg38.150200.bed.split6243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6244 0 1 2 100 hg38.150200.bed.split6244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6245 0 1 2 100 hg38.150200.bed.split6245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6246 0 1 2 100 hg38.150200.bed.split6246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6247 0 1 2 100 hg38.150200.bed.split6247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6248 0 1 2 100 hg38.150200.bed.split6248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6249 0 1 2 100 hg38.150200.bed.split6249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split625 0 1 2 100 hg38.150200.bed.split625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6250 0 1 2 100 hg38.150200.bed.split6250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6251 0 1 2 100 hg38.150200.bed.split6251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6252 0 1 2 100 hg38.150200.bed.split6252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6253 0 1 2 100 hg38.150200.bed.split6253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6254 0 1 2 100 hg38.150200.bed.split6254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6255 0 1 2 100 hg38.150200.bed.split6255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6256 0 1 2 100 hg38.150200.bed.split6256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6257 0 1 2 100 hg38.150200.bed.split6257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6258 0 1 2 100 hg38.150200.bed.split6258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6259 0 1 2 100 hg38.150200.bed.split6259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split626 0 1 2 100 hg38.150200.bed.split626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6260 0 1 2 100 hg38.150200.bed.split6260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6261 0 1 2 100 hg38.150200.bed.split6261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6262 0 1 2 100 hg38.150200.bed.split6262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6263 0 1 2 100 hg38.150200.bed.split6263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6264 0 1 2 100 hg38.150200.bed.split6264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6265 0 1 2 100 hg38.150200.bed.split6265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6266 0 1 2 100 hg38.150200.bed.split6266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6267 0 1 2 100 hg38.150200.bed.split6267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6268 0 1 2 100 hg38.150200.bed.split6268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6269 0 1 2 100 hg38.150200.bed.split6269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split627 0 1 2 100 hg38.150200.bed.split627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6270 0 1 2 100 hg38.150200.bed.split6270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6271 0 1 2 100 hg38.150200.bed.split6271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6272 0 1 2 100 hg38.150200.bed.split6272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6273 0 1 2 100 hg38.150200.bed.split6273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6274 0 1 2 100 hg38.150200.bed.split6274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6275 0 1 2 100 hg38.150200.bed.split6275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6276 0 1 2 100 hg38.150200.bed.split6276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6277 0 1 2 100 hg38.150200.bed.split6277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6278 0 1 2 100 hg38.150200.bed.split6278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6279 0 1 2 100 hg38.150200.bed.split6279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split628 0 1 2 100 hg38.150200.bed.split628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6280 0 1 2 100 hg38.150200.bed.split6280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6281 0 1 2 100 hg38.150200.bed.split6281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6282 0 1 2 100 hg38.150200.bed.split6282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6283 0 1 2 100 hg38.150200.bed.split6283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6284 0 1 2 100 hg38.150200.bed.split6284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6285 0 1 2 100 hg38.150200.bed.split6285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6286 0 1 2 100 hg38.150200.bed.split6286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6287 0 1 2 100 hg38.150200.bed.split6287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6288 0 1 2 100 hg38.150200.bed.split6288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6289 0 1 2 100 hg38.150200.bed.split6289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split629 0 1 2 100 hg38.150200.bed.split629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6290 0 1 2 100 hg38.150200.bed.split6290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6291 0 1 2 100 hg38.150200.bed.split6291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6292 0 1 2 100 hg38.150200.bed.split6292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6293 0 1 2 100 hg38.150200.bed.split6293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6294 0 1 2 100 hg38.150200.bed.split6294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6295 0 1 2 100 hg38.150200.bed.split6295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6296 0 1 2 100 hg38.150200.bed.split6296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6297 0 1 2 100 hg38.150200.bed.split6297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6298 0 1 2 100 hg38.150200.bed.split6298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6299 0 1 2 100 hg38.150200.bed.split6299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split63 0 1 2 100 hg38.150200.bed.split63.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split630 0 1 2 100 hg38.150200.bed.split630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6300 0 1 2 100 hg38.150200.bed.split6300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6301 0 1 2 100 hg38.150200.bed.split6301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6302 0 1 2 100 hg38.150200.bed.split6302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6303 0 1 2 100 hg38.150200.bed.split6303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6304 0 1 2 100 hg38.150200.bed.split6304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6305 0 1 2 100 hg38.150200.bed.split6305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6306 0 1 2 100 hg38.150200.bed.split6306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6307 0 1 2 100 hg38.150200.bed.split6307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6308 0 1 2 100 hg38.150200.bed.split6308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6309 0 1 2 100 hg38.150200.bed.split6309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split631 0 1 2 100 hg38.150200.bed.split631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6310 0 1 2 100 hg38.150200.bed.split6310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6311 0 1 2 100 hg38.150200.bed.split6311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6312 0 1 2 100 hg38.150200.bed.split6312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6313 0 1 2 100 hg38.150200.bed.split6313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6314 0 1 2 100 hg38.150200.bed.split6314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6315 0 1 2 100 hg38.150200.bed.split6315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6316 0 1 2 100 hg38.150200.bed.split6316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6317 0 1 2 100 hg38.150200.bed.split6317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6318 0 1 2 100 hg38.150200.bed.split6318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6319 0 1 2 100 hg38.150200.bed.split6319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split632 0 1 2 100 hg38.150200.bed.split632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6320 0 1 2 100 hg38.150200.bed.split6320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6321 0 1 2 100 hg38.150200.bed.split6321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6322 0 1 2 100 hg38.150200.bed.split6322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6323 0 1 2 100 hg38.150200.bed.split6323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6324 0 1 2 100 hg38.150200.bed.split6324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6325 0 1 2 100 hg38.150200.bed.split6325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6326 0 1 2 100 hg38.150200.bed.split6326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6327 0 1 2 100 hg38.150200.bed.split6327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6328 0 1 2 100 hg38.150200.bed.split6328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6329 0 1 2 100 hg38.150200.bed.split6329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split633 0 1 2 100 hg38.150200.bed.split633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6330 0 1 2 100 hg38.150200.bed.split6330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6331 0 1 2 100 hg38.150200.bed.split6331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6332 0 1 2 100 hg38.150200.bed.split6332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6333 0 1 2 100 hg38.150200.bed.split6333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6334 0 1 2 100 hg38.150200.bed.split6334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6335 0 1 2 100 hg38.150200.bed.split6335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6336 0 1 2 100 hg38.150200.bed.split6336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6337 0 1 2 100 hg38.150200.bed.split6337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6338 0 1 2 100 hg38.150200.bed.split6338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6339 0 1 2 100 hg38.150200.bed.split6339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split634 0 1 2 100 hg38.150200.bed.split634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6340 0 1 2 100 hg38.150200.bed.split6340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6341 0 1 2 100 hg38.150200.bed.split6341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6342 0 1 2 100 hg38.150200.bed.split6342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6343 0 1 2 100 hg38.150200.bed.split6343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6344 0 1 2 100 hg38.150200.bed.split6344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6345 0 1 2 100 hg38.150200.bed.split6345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6346 0 1 2 100 hg38.150200.bed.split6346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6347 0 1 2 100 hg38.150200.bed.split6347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6348 0 1 2 100 hg38.150200.bed.split6348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6349 0 1 2 100 hg38.150200.bed.split6349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split635 0 1 2 100 hg38.150200.bed.split635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6350 0 1 2 100 hg38.150200.bed.split6350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6351 0 1 2 100 hg38.150200.bed.split6351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6352 0 1 2 100 hg38.150200.bed.split6352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6353 0 1 2 100 hg38.150200.bed.split6353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6354 0 1 2 100 hg38.150200.bed.split6354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6355 0 1 2 100 hg38.150200.bed.split6355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6356 0 1 2 100 hg38.150200.bed.split6356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6357 0 1 2 100 hg38.150200.bed.split6357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6358 0 1 2 100 hg38.150200.bed.split6358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6359 0 1 2 100 hg38.150200.bed.split6359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split636 0 1 2 100 hg38.150200.bed.split636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6360 0 1 2 100 hg38.150200.bed.split6360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6361 0 1 2 100 hg38.150200.bed.split6361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6362 0 1 2 100 hg38.150200.bed.split6362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6363 0 1 2 100 hg38.150200.bed.split6363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6364 0 1 2 100 hg38.150200.bed.split6364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6365 0 1 2 100 hg38.150200.bed.split6365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6366 0 1 2 100 hg38.150200.bed.split6366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6367 0 1 2 100 hg38.150200.bed.split6367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6368 0 1 2 100 hg38.150200.bed.split6368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6369 0 1 2 100 hg38.150200.bed.split6369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split637 0 1 2 100 hg38.150200.bed.split637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6370 0 1 2 100 hg38.150200.bed.split6370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6371 0 1 2 100 hg38.150200.bed.split6371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6372 0 1 2 100 hg38.150200.bed.split6372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6373 0 1 2 100 hg38.150200.bed.split6373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6374 0 1 2 100 hg38.150200.bed.split6374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6375 0 1 2 100 hg38.150200.bed.split6375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6376 0 1 2 100 hg38.150200.bed.split6376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6377 0 1 2 100 hg38.150200.bed.split6377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6378 0 1 2 100 hg38.150200.bed.split6378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6379 0 1 2 100 hg38.150200.bed.split6379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split638 0 1 2 100 hg38.150200.bed.split638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6380 0 1 2 100 hg38.150200.bed.split6380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6381 0 1 2 100 hg38.150200.bed.split6381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6382 0 1 2 100 hg38.150200.bed.split6382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6383 0 1 2 100 hg38.150200.bed.split6383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6384 0 1 2 100 hg38.150200.bed.split6384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6385 0 1 2 100 hg38.150200.bed.split6385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6386 0 1 2 100 hg38.150200.bed.split6386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6387 0 1 2 100 hg38.150200.bed.split6387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6388 0 1 2 100 hg38.150200.bed.split6388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6389 0 1 2 100 hg38.150200.bed.split6389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split639 0 1 2 100 hg38.150200.bed.split639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6390 0 1 2 100 hg38.150200.bed.split6390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6391 0 1 2 100 hg38.150200.bed.split6391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6392 0 1 2 100 hg38.150200.bed.split6392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6393 0 1 2 100 hg38.150200.bed.split6393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6394 0 1 2 100 hg38.150200.bed.split6394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6395 0 1 2 100 hg38.150200.bed.split6395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6396 0 1 2 100 hg38.150200.bed.split6396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6397 0 1 2 100 hg38.150200.bed.split6397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6398 0 1 2 100 hg38.150200.bed.split6398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6399 0 1 2 100 hg38.150200.bed.split6399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split64 0 1 2 100 hg38.150200.bed.split64.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split640 0 1 2 100 hg38.150200.bed.split640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6400 0 1 2 100 hg38.150200.bed.split6400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6401 0 1 2 100 hg38.150200.bed.split6401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6402 0 1 2 100 hg38.150200.bed.split6402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6403 0 1 2 100 hg38.150200.bed.split6403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6404 0 1 2 100 hg38.150200.bed.split6404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6405 0 1 2 100 hg38.150200.bed.split6405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6406 0 1 2 100 hg38.150200.bed.split6406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6407 0 1 2 100 hg38.150200.bed.split6407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6408 0 1 2 100 hg38.150200.bed.split6408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6409 0 1 2 100 hg38.150200.bed.split6409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split641 0 1 2 100 hg38.150200.bed.split641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6410 0 1 2 100 hg38.150200.bed.split6410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6411 0 1 2 100 hg38.150200.bed.split6411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6412 0 1 2 100 hg38.150200.bed.split6412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6413 0 1 2 100 hg38.150200.bed.split6413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6414 0 1 2 100 hg38.150200.bed.split6414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6415 0 1 2 100 hg38.150200.bed.split6415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6416 0 1 2 100 hg38.150200.bed.split6416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6417 0 1 2 100 hg38.150200.bed.split6417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6418 0 1 2 100 hg38.150200.bed.split6418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6419 0 1 2 100 hg38.150200.bed.split6419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split642 0 1 2 100 hg38.150200.bed.split642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6420 0 1 2 100 hg38.150200.bed.split6420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6421 0 1 2 100 hg38.150200.bed.split6421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6422 0 1 2 100 hg38.150200.bed.split6422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6423 0 1 2 100 hg38.150200.bed.split6423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6424 0 1 2 100 hg38.150200.bed.split6424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6425 0 1 2 100 hg38.150200.bed.split6425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6426 0 1 2 100 hg38.150200.bed.split6426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6427 0 1 2 100 hg38.150200.bed.split6427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6428 0 1 2 100 hg38.150200.bed.split6428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6429 0 1 2 100 hg38.150200.bed.split6429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split643 0 1 2 100 hg38.150200.bed.split643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6430 0 1 2 100 hg38.150200.bed.split6430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6431 0 1 2 100 hg38.150200.bed.split6431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6432 0 1 2 100 hg38.150200.bed.split6432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6433 0 1 2 100 hg38.150200.bed.split6433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6434 0 1 2 100 hg38.150200.bed.split6434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6435 0 1 2 100 hg38.150200.bed.split6435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6436 0 1 2 100 hg38.150200.bed.split6436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6437 0 1 2 100 hg38.150200.bed.split6437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6438 0 1 2 100 hg38.150200.bed.split6438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6439 0 1 2 100 hg38.150200.bed.split6439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split644 0 1 2 100 hg38.150200.bed.split644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6440 0 1 2 100 hg38.150200.bed.split6440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6441 0 1 2 100 hg38.150200.bed.split6441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6442 0 1 2 100 hg38.150200.bed.split6442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6443 0 1 2 100 hg38.150200.bed.split6443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6444 0 1 2 100 hg38.150200.bed.split6444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6445 0 1 2 100 hg38.150200.bed.split6445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6446 0 1 2 100 hg38.150200.bed.split6446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6447 0 1 2 100 hg38.150200.bed.split6447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6448 0 1 2 100 hg38.150200.bed.split6448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6449 0 1 2 100 hg38.150200.bed.split6449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split645 0 1 2 100 hg38.150200.bed.split645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6450 0 1 2 100 hg38.150200.bed.split6450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6451 0 1 2 100 hg38.150200.bed.split6451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6452 0 1 2 100 hg38.150200.bed.split6452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6453 0 1 2 100 hg38.150200.bed.split6453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6454 0 1 2 100 hg38.150200.bed.split6454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6455 0 1 2 100 hg38.150200.bed.split6455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6456 0 1 2 100 hg38.150200.bed.split6456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6457 0 1 2 100 hg38.150200.bed.split6457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6458 0 1 2 100 hg38.150200.bed.split6458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6459 0 1 2 100 hg38.150200.bed.split6459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split646 0 1 2 100 hg38.150200.bed.split646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6460 0 1 2 100 hg38.150200.bed.split6460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6461 0 1 2 100 hg38.150200.bed.split6461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6462 0 1 2 100 hg38.150200.bed.split6462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6463 0 1 2 100 hg38.150200.bed.split6463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6464 0 1 2 100 hg38.150200.bed.split6464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6465 0 1 2 100 hg38.150200.bed.split6465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6466 0 1 2 100 hg38.150200.bed.split6466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6467 0 1 2 100 hg38.150200.bed.split6467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6468 0 1 2 100 hg38.150200.bed.split6468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6469 0 1 2 100 hg38.150200.bed.split6469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split647 0 1 2 100 hg38.150200.bed.split647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6470 0 1 2 100 hg38.150200.bed.split6470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6471 0 1 2 100 hg38.150200.bed.split6471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6472 0 1 2 100 hg38.150200.bed.split6472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6473 0 1 2 100 hg38.150200.bed.split6473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6474 0 1 2 100 hg38.150200.bed.split6474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6475 0 1 2 100 hg38.150200.bed.split6475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6476 0 1 2 100 hg38.150200.bed.split6476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6477 0 1 2 100 hg38.150200.bed.split6477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6478 0 1 2 100 hg38.150200.bed.split6478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6479 0 1 2 100 hg38.150200.bed.split6479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split648 0 1 2 100 hg38.150200.bed.split648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6480 0 1 2 100 hg38.150200.bed.split6480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6481 0 1 2 100 hg38.150200.bed.split6481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6482 0 1 2 100 hg38.150200.bed.split6482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6483 0 1 2 100 hg38.150200.bed.split6483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6484 0 1 2 100 hg38.150200.bed.split6484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6485 0 1 2 100 hg38.150200.bed.split6485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6486 0 1 2 100 hg38.150200.bed.split6486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6487 0 1 2 100 hg38.150200.bed.split6487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6488 0 1 2 100 hg38.150200.bed.split6488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6489 0 1 2 100 hg38.150200.bed.split6489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split649 0 1 2 100 hg38.150200.bed.split649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6490 0 1 2 100 hg38.150200.bed.split6490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6491 0 1 2 100 hg38.150200.bed.split6491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6492 0 1 2 100 hg38.150200.bed.split6492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6493 0 1 2 100 hg38.150200.bed.split6493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6494 0 1 2 100 hg38.150200.bed.split6494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6495 0 1 2 100 hg38.150200.bed.split6495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6496 0 1 2 100 hg38.150200.bed.split6496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6497 0 1 2 100 hg38.150200.bed.split6497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6498 0 1 2 100 hg38.150200.bed.split6498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6499 0 1 2 100 hg38.150200.bed.split6499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split65 0 1 2 100 hg38.150200.bed.split65.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split650 0 1 2 100 hg38.150200.bed.split650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6500 0 1 2 100 hg38.150200.bed.split6500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6501 0 1 2 100 hg38.150200.bed.split6501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6502 0 1 2 100 hg38.150200.bed.split6502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6503 0 1 2 100 hg38.150200.bed.split6503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6504 0 1 2 100 hg38.150200.bed.split6504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6505 0 1 2 100 hg38.150200.bed.split6505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6506 0 1 2 100 hg38.150200.bed.split6506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6507 0 1 2 100 hg38.150200.bed.split6507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6508 0 1 2 100 hg38.150200.bed.split6508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6509 0 1 2 100 hg38.150200.bed.split6509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split651 0 1 2 100 hg38.150200.bed.split651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6510 0 1 2 100 hg38.150200.bed.split6510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6511 0 1 2 100 hg38.150200.bed.split6511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6512 0 1 2 100 hg38.150200.bed.split6512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6513 0 1 2 100 hg38.150200.bed.split6513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6514 0 1 2 100 hg38.150200.bed.split6514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6515 0 1 2 100 hg38.150200.bed.split6515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6516 0 1 2 100 hg38.150200.bed.split6516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6517 0 1 2 100 hg38.150200.bed.split6517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6518 0 1 2 100 hg38.150200.bed.split6518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6519 0 1 2 100 hg38.150200.bed.split6519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split652 0 1 2 100 hg38.150200.bed.split652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6520 0 1 2 100 hg38.150200.bed.split6520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6521 0 1 2 100 hg38.150200.bed.split6521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6522 0 1 2 100 hg38.150200.bed.split6522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6523 0 1 2 100 hg38.150200.bed.split6523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6524 0 1 2 100 hg38.150200.bed.split6524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6525 0 1 2 100 hg38.150200.bed.split6525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6526 0 1 2 100 hg38.150200.bed.split6526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6527 0 1 2 100 hg38.150200.bed.split6527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6528 0 1 2 100 hg38.150200.bed.split6528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6529 0 1 2 100 hg38.150200.bed.split6529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split653 0 1 2 100 hg38.150200.bed.split653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6530 0 1 2 100 hg38.150200.bed.split6530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6531 0 1 2 100 hg38.150200.bed.split6531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6532 0 1 2 100 hg38.150200.bed.split6532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6533 0 1 2 100 hg38.150200.bed.split6533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6534 0 1 2 100 hg38.150200.bed.split6534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6535 0 1 2 100 hg38.150200.bed.split6535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6536 0 1 2 100 hg38.150200.bed.split6536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6537 0 1 2 100 hg38.150200.bed.split6537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6538 0 1 2 100 hg38.150200.bed.split6538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6539 0 1 2 100 hg38.150200.bed.split6539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split654 0 1 2 100 hg38.150200.bed.split654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6540 0 1 2 100 hg38.150200.bed.split6540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6541 0 1 2 100 hg38.150200.bed.split6541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6542 0 1 2 100 hg38.150200.bed.split6542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6543 0 1 2 100 hg38.150200.bed.split6543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6544 0 1 2 100 hg38.150200.bed.split6544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6545 0 1 2 100 hg38.150200.bed.split6545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6546 0 1 2 100 hg38.150200.bed.split6546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6547 0 1 2 100 hg38.150200.bed.split6547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6548 0 1 2 100 hg38.150200.bed.split6548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6549 0 1 2 100 hg38.150200.bed.split6549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split655 0 1 2 100 hg38.150200.bed.split655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6550 0 1 2 100 hg38.150200.bed.split6550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6551 0 1 2 100 hg38.150200.bed.split6551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6552 0 1 2 100 hg38.150200.bed.split6552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6553 0 1 2 100 hg38.150200.bed.split6553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6554 0 1 2 100 hg38.150200.bed.split6554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6555 0 1 2 100 hg38.150200.bed.split6555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6556 0 1 2 100 hg38.150200.bed.split6556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6557 0 1 2 100 hg38.150200.bed.split6557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6558 0 1 2 100 hg38.150200.bed.split6558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6559 0 1 2 100 hg38.150200.bed.split6559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split656 0 1 2 100 hg38.150200.bed.split656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6560 0 1 2 100 hg38.150200.bed.split6560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6561 0 1 2 100 hg38.150200.bed.split6561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6562 0 1 2 100 hg38.150200.bed.split6562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6563 0 1 2 100 hg38.150200.bed.split6563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6564 0 1 2 100 hg38.150200.bed.split6564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6565 0 1 2 100 hg38.150200.bed.split6565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6566 0 1 2 100 hg38.150200.bed.split6566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6567 0 1 2 100 hg38.150200.bed.split6567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6568 0 1 2 100 hg38.150200.bed.split6568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6569 0 1 2 100 hg38.150200.bed.split6569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split657 0 1 2 100 hg38.150200.bed.split657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6570 0 1 2 100 hg38.150200.bed.split6570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6571 0 1 2 100 hg38.150200.bed.split6571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6572 0 1 2 100 hg38.150200.bed.split6572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6573 0 1 2 100 hg38.150200.bed.split6573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6574 0 1 2 100 hg38.150200.bed.split6574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6575 0 1 2 100 hg38.150200.bed.split6575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6576 0 1 2 100 hg38.150200.bed.split6576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6577 0 1 2 100 hg38.150200.bed.split6577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6578 0 1 2 100 hg38.150200.bed.split6578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6579 0 1 2 100 hg38.150200.bed.split6579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split658 0 1 2 100 hg38.150200.bed.split658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6580 0 1 2 100 hg38.150200.bed.split6580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6581 0 1 2 100 hg38.150200.bed.split6581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6582 0 1 2 100 hg38.150200.bed.split6582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6583 0 1 2 100 hg38.150200.bed.split6583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6584 0 1 2 100 hg38.150200.bed.split6584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6585 0 1 2 100 hg38.150200.bed.split6585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6586 0 1 2 100 hg38.150200.bed.split6586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6587 0 1 2 100 hg38.150200.bed.split6587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6588 0 1 2 100 hg38.150200.bed.split6588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6589 0 1 2 100 hg38.150200.bed.split6589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split659 0 1 2 100 hg38.150200.bed.split659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6590 0 1 2 100 hg38.150200.bed.split6590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6591 0 1 2 100 hg38.150200.bed.split6591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6592 0 1 2 100 hg38.150200.bed.split6592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6593 0 1 2 100 hg38.150200.bed.split6593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6594 0 1 2 100 hg38.150200.bed.split6594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6595 0 1 2 100 hg38.150200.bed.split6595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6596 0 1 2 100 hg38.150200.bed.split6596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6597 0 1 2 100 hg38.150200.bed.split6597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6598 0 1 2 100 hg38.150200.bed.split6598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6599 0 1 2 100 hg38.150200.bed.split6599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split66 0 1 2 100 hg38.150200.bed.split66.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split660 0 1 2 100 hg38.150200.bed.split660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6600 0 1 2 100 hg38.150200.bed.split6600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6601 0 1 2 100 hg38.150200.bed.split6601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6602 0 1 2 100 hg38.150200.bed.split6602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6603 0 1 2 100 hg38.150200.bed.split6603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6604 0 1 2 100 hg38.150200.bed.split6604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6605 0 1 2 100 hg38.150200.bed.split6605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6606 0 1 2 100 hg38.150200.bed.split6606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6607 0 1 2 100 hg38.150200.bed.split6607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6608 0 1 2 100 hg38.150200.bed.split6608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6609 0 1 2 100 hg38.150200.bed.split6609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split661 0 1 2 100 hg38.150200.bed.split661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6610 0 1 2 100 hg38.150200.bed.split6610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6611 0 1 2 100 hg38.150200.bed.split6611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6612 0 1 2 100 hg38.150200.bed.split6612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6613 0 1 2 100 hg38.150200.bed.split6613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6614 0 1 2 100 hg38.150200.bed.split6614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6615 0 1 2 100 hg38.150200.bed.split6615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6616 0 1 2 100 hg38.150200.bed.split6616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6617 0 1 2 100 hg38.150200.bed.split6617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6618 0 1 2 100 hg38.150200.bed.split6618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6619 0 1 2 100 hg38.150200.bed.split6619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split662 0 1 2 100 hg38.150200.bed.split662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6620 0 1 2 100 hg38.150200.bed.split6620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6621 0 1 2 100 hg38.150200.bed.split6621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6622 0 1 2 100 hg38.150200.bed.split6622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6623 0 1 2 100 hg38.150200.bed.split6623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6624 0 1 2 100 hg38.150200.bed.split6624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6625 0 1 2 100 hg38.150200.bed.split6625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6626 0 1 2 100 hg38.150200.bed.split6626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6627 0 1 2 100 hg38.150200.bed.split6627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6628 0 1 2 100 hg38.150200.bed.split6628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6629 0 1 2 100 hg38.150200.bed.split6629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split663 0 1 2 100 hg38.150200.bed.split663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6630 0 1 2 100 hg38.150200.bed.split6630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6631 0 1 2 100 hg38.150200.bed.split6631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6632 0 1 2 100 hg38.150200.bed.split6632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6633 0 1 2 100 hg38.150200.bed.split6633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6634 0 1 2 100 hg38.150200.bed.split6634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6635 0 1 2 100 hg38.150200.bed.split6635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6636 0 1 2 100 hg38.150200.bed.split6636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6637 0 1 2 100 hg38.150200.bed.split6637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6638 0 1 2 100 hg38.150200.bed.split6638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6639 0 1 2 100 hg38.150200.bed.split6639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split664 0 1 2 100 hg38.150200.bed.split664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6640 0 1 2 100 hg38.150200.bed.split6640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6641 0 1 2 100 hg38.150200.bed.split6641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6642 0 1 2 100 hg38.150200.bed.split6642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6643 0 1 2 100 hg38.150200.bed.split6643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6644 0 1 2 100 hg38.150200.bed.split6644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6645 0 1 2 100 hg38.150200.bed.split6645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6646 0 1 2 100 hg38.150200.bed.split6646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6647 0 1 2 100 hg38.150200.bed.split6647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6648 0 1 2 100 hg38.150200.bed.split6648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6649 0 1 2 100 hg38.150200.bed.split6649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split665 0 1 2 100 hg38.150200.bed.split665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6650 0 1 2 100 hg38.150200.bed.split6650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6651 0 1 2 100 hg38.150200.bed.split6651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6652 0 1 2 100 hg38.150200.bed.split6652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6653 0 1 2 100 hg38.150200.bed.split6653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6654 0 1 2 100 hg38.150200.bed.split6654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6655 0 1 2 100 hg38.150200.bed.split6655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6656 0 1 2 100 hg38.150200.bed.split6656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6657 0 1 2 100 hg38.150200.bed.split6657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6658 0 1 2 100 hg38.150200.bed.split6658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6659 0 1 2 100 hg38.150200.bed.split6659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split666 0 1 2 100 hg38.150200.bed.split666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6660 0 1 2 100 hg38.150200.bed.split6660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6661 0 1 2 100 hg38.150200.bed.split6661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6662 0 1 2 100 hg38.150200.bed.split6662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6663 0 1 2 100 hg38.150200.bed.split6663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6664 0 1 2 100 hg38.150200.bed.split6664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6665 0 1 2 100 hg38.150200.bed.split6665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6666 0 1 2 100 hg38.150200.bed.split6666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6667 0 1 2 100 hg38.150200.bed.split6667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6668 0 1 2 100 hg38.150200.bed.split6668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6669 0 1 2 100 hg38.150200.bed.split6669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split667 0 1 2 100 hg38.150200.bed.split667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6670 0 1 2 100 hg38.150200.bed.split6670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6671 0 1 2 100 hg38.150200.bed.split6671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6672 0 1 2 100 hg38.150200.bed.split6672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6673 0 1 2 100 hg38.150200.bed.split6673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6674 0 1 2 100 hg38.150200.bed.split6674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6675 0 1 2 100 hg38.150200.bed.split6675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6676 0 1 2 100 hg38.150200.bed.split6676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6677 0 1 2 100 hg38.150200.bed.split6677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6678 0 1 2 100 hg38.150200.bed.split6678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6679 0 1 2 100 hg38.150200.bed.split6679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split668 0 1 2 100 hg38.150200.bed.split668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6680 0 1 2 100 hg38.150200.bed.split6680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6681 0 1 2 100 hg38.150200.bed.split6681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6682 0 1 2 100 hg38.150200.bed.split6682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6683 0 1 2 100 hg38.150200.bed.split6683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6684 0 1 2 100 hg38.150200.bed.split6684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6685 0 1 2 100 hg38.150200.bed.split6685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6686 0 1 2 100 hg38.150200.bed.split6686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6687 0 1 2 100 hg38.150200.bed.split6687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6688 0 1 2 100 hg38.150200.bed.split6688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6689 0 1 2 100 hg38.150200.bed.split6689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split669 0 1 2 100 hg38.150200.bed.split669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6690 0 1 2 100 hg38.150200.bed.split6690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6691 0 1 2 100 hg38.150200.bed.split6691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6692 0 1 2 100 hg38.150200.bed.split6692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6693 0 1 2 100 hg38.150200.bed.split6693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6694 0 1 2 100 hg38.150200.bed.split6694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6695 0 1 2 100 hg38.150200.bed.split6695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6696 0 1 2 100 hg38.150200.bed.split6696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6697 0 1 2 100 hg38.150200.bed.split6697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6698 0 1 2 100 hg38.150200.bed.split6698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6699 0 1 2 100 hg38.150200.bed.split6699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split67 0 1 2 100 hg38.150200.bed.split67.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split670 0 1 2 100 hg38.150200.bed.split670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6700 0 1 2 100 hg38.150200.bed.split6700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6701 0 1 2 100 hg38.150200.bed.split6701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6702 0 1 2 100 hg38.150200.bed.split6702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6703 0 1 2 100 hg38.150200.bed.split6703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6704 0 1 2 100 hg38.150200.bed.split6704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6705 0 1 2 100 hg38.150200.bed.split6705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6706 0 1 2 100 hg38.150200.bed.split6706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6707 0 1 2 100 hg38.150200.bed.split6707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6708 0 1 2 100 hg38.150200.bed.split6708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6709 0 1 2 100 hg38.150200.bed.split6709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split671 0 1 2 100 hg38.150200.bed.split671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6710 0 1 2 100 hg38.150200.bed.split6710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6711 0 1 2 100 hg38.150200.bed.split6711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6712 0 1 2 100 hg38.150200.bed.split6712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6713 0 1 2 100 hg38.150200.bed.split6713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6714 0 1 2 100 hg38.150200.bed.split6714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6715 0 1 2 100 hg38.150200.bed.split6715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6716 0 1 2 100 hg38.150200.bed.split6716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6717 0 1 2 100 hg38.150200.bed.split6717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6718 0 1 2 100 hg38.150200.bed.split6718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6719 0 1 2 100 hg38.150200.bed.split6719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split672 0 1 2 100 hg38.150200.bed.split672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6720 0 1 2 100 hg38.150200.bed.split6720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6721 0 1 2 100 hg38.150200.bed.split6721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6722 0 1 2 100 hg38.150200.bed.split6722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6723 0 1 2 100 hg38.150200.bed.split6723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6724 0 1 2 100 hg38.150200.bed.split6724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6725 0 1 2 100 hg38.150200.bed.split6725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6726 0 1 2 100 hg38.150200.bed.split6726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6727 0 1 2 100 hg38.150200.bed.split6727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6728 0 1 2 100 hg38.150200.bed.split6728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6729 0 1 2 100 hg38.150200.bed.split6729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split673 0 1 2 100 hg38.150200.bed.split673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6730 0 1 2 100 hg38.150200.bed.split6730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6731 0 1 2 100 hg38.150200.bed.split6731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6732 0 1 2 100 hg38.150200.bed.split6732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6733 0 1 2 100 hg38.150200.bed.split6733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6734 0 1 2 100 hg38.150200.bed.split6734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6735 0 1 2 100 hg38.150200.bed.split6735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6736 0 1 2 100 hg38.150200.bed.split6736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6737 0 1 2 100 hg38.150200.bed.split6737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6738 0 1 2 100 hg38.150200.bed.split6738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6739 0 1 2 100 hg38.150200.bed.split6739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split674 0 1 2 100 hg38.150200.bed.split674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6740 0 1 2 100 hg38.150200.bed.split6740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6741 0 1 2 100 hg38.150200.bed.split6741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6742 0 1 2 100 hg38.150200.bed.split6742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6743 0 1 2 100 hg38.150200.bed.split6743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6744 0 1 2 100 hg38.150200.bed.split6744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6745 0 1 2 100 hg38.150200.bed.split6745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6746 0 1 2 100 hg38.150200.bed.split6746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6747 0 1 2 100 hg38.150200.bed.split6747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6748 0 1 2 100 hg38.150200.bed.split6748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6749 0 1 2 100 hg38.150200.bed.split6749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split675 0 1 2 100 hg38.150200.bed.split675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6750 0 1 2 100 hg38.150200.bed.split6750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6751 0 1 2 100 hg38.150200.bed.split6751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6752 0 1 2 100 hg38.150200.bed.split6752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6753 0 1 2 100 hg38.150200.bed.split6753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6754 0 1 2 100 hg38.150200.bed.split6754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6755 0 1 2 100 hg38.150200.bed.split6755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6756 0 1 2 100 hg38.150200.bed.split6756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6757 0 1 2 100 hg38.150200.bed.split6757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6758 0 1 2 100 hg38.150200.bed.split6758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6759 0 1 2 100 hg38.150200.bed.split6759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split676 0 1 2 100 hg38.150200.bed.split676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6760 0 1 2 100 hg38.150200.bed.split6760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6761 0 1 2 100 hg38.150200.bed.split6761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6762 0 1 2 100 hg38.150200.bed.split6762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6763 0 1 2 100 hg38.150200.bed.split6763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6764 0 1 2 100 hg38.150200.bed.split6764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6765 0 1 2 100 hg38.150200.bed.split6765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6766 0 1 2 100 hg38.150200.bed.split6766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6767 0 1 2 100 hg38.150200.bed.split6767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6768 0 1 2 100 hg38.150200.bed.split6768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6769 0 1 2 100 hg38.150200.bed.split6769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split677 0 1 2 100 hg38.150200.bed.split677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6770 0 1 2 100 hg38.150200.bed.split6770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6771 0 1 2 100 hg38.150200.bed.split6771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6772 0 1 2 100 hg38.150200.bed.split6772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6773 0 1 2 100 hg38.150200.bed.split6773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6774 0 1 2 100 hg38.150200.bed.split6774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6775 0 1 2 100 hg38.150200.bed.split6775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6776 0 1 2 100 hg38.150200.bed.split6776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6777 0 1 2 100 hg38.150200.bed.split6777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6778 0 1 2 100 hg38.150200.bed.split6778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6779 0 1 2 100 hg38.150200.bed.split6779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split678 0 1 2 100 hg38.150200.bed.split678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6780 0 1 2 100 hg38.150200.bed.split6780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6781 0 1 2 100 hg38.150200.bed.split6781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6782 0 1 2 100 hg38.150200.bed.split6782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6783 0 1 2 100 hg38.150200.bed.split6783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6784 0 1 2 100 hg38.150200.bed.split6784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6785 0 1 2 100 hg38.150200.bed.split6785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6786 0 1 2 100 hg38.150200.bed.split6786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6787 0 1 2 100 hg38.150200.bed.split6787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6788 0 1 2 100 hg38.150200.bed.split6788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6789 0 1 2 100 hg38.150200.bed.split6789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split679 0 1 2 100 hg38.150200.bed.split679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6790 0 1 2 100 hg38.150200.bed.split6790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6791 0 1 2 100 hg38.150200.bed.split6791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6792 0 1 2 100 hg38.150200.bed.split6792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6793 0 1 2 100 hg38.150200.bed.split6793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6794 0 1 2 100 hg38.150200.bed.split6794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6795 0 1 2 100 hg38.150200.bed.split6795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6796 0 1 2 100 hg38.150200.bed.split6796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6797 0 1 2 100 hg38.150200.bed.split6797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6798 0 1 2 100 hg38.150200.bed.split6798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6799 0 1 2 100 hg38.150200.bed.split6799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split68 0 1 2 100 hg38.150200.bed.split68.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split680 0 1 2 100 hg38.150200.bed.split680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6800 0 1 2 100 hg38.150200.bed.split6800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6801 0 1 2 100 hg38.150200.bed.split6801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6802 0 1 2 100 hg38.150200.bed.split6802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6803 0 1 2 100 hg38.150200.bed.split6803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6804 0 1 2 100 hg38.150200.bed.split6804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6805 0 1 2 100 hg38.150200.bed.split6805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6806 0 1 2 100 hg38.150200.bed.split6806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6807 0 1 2 100 hg38.150200.bed.split6807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6808 0 1 2 100 hg38.150200.bed.split6808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6809 0 1 2 100 hg38.150200.bed.split6809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split681 0 1 2 100 hg38.150200.bed.split681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6810 0 1 2 100 hg38.150200.bed.split6810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6811 0 1 2 100 hg38.150200.bed.split6811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6812 0 1 2 100 hg38.150200.bed.split6812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6813 0 1 2 100 hg38.150200.bed.split6813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6814 0 1 2 100 hg38.150200.bed.split6814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6815 0 1 2 100 hg38.150200.bed.split6815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6816 0 1 2 100 hg38.150200.bed.split6816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6817 0 1 2 100 hg38.150200.bed.split6817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6818 0 1 2 100 hg38.150200.bed.split6818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6819 0 1 2 100 hg38.150200.bed.split6819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split682 0 1 2 100 hg38.150200.bed.split682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6820 0 1 2 100 hg38.150200.bed.split6820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6821 0 1 2 100 hg38.150200.bed.split6821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6822 0 1 2 100 hg38.150200.bed.split6822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6823 0 1 2 100 hg38.150200.bed.split6823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6824 0 1 2 100 hg38.150200.bed.split6824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6825 0 1 2 100 hg38.150200.bed.split6825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6826 0 1 2 100 hg38.150200.bed.split6826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6827 0 1 2 100 hg38.150200.bed.split6827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6828 0 1 2 100 hg38.150200.bed.split6828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6829 0 1 2 100 hg38.150200.bed.split6829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split683 0 1 2 100 hg38.150200.bed.split683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6830 0 1 2 100 hg38.150200.bed.split6830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6831 0 1 2 100 hg38.150200.bed.split6831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6832 0 1 2 100 hg38.150200.bed.split6832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6833 0 1 2 100 hg38.150200.bed.split6833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6834 0 1 2 100 hg38.150200.bed.split6834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6835 0 1 2 100 hg38.150200.bed.split6835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6836 0 1 2 100 hg38.150200.bed.split6836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6837 0 1 2 100 hg38.150200.bed.split6837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6838 0 1 2 100 hg38.150200.bed.split6838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6839 0 1 2 100 hg38.150200.bed.split6839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split684 0 1 2 100 hg38.150200.bed.split684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6840 0 1 2 100 hg38.150200.bed.split6840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6841 0 1 2 100 hg38.150200.bed.split6841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6842 0 1 2 100 hg38.150200.bed.split6842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6843 0 1 2 100 hg38.150200.bed.split6843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6844 0 1 2 100 hg38.150200.bed.split6844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6845 0 1 2 100 hg38.150200.bed.split6845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6846 0 1 2 100 hg38.150200.bed.split6846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6847 0 1 2 100 hg38.150200.bed.split6847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6848 0 1 2 100 hg38.150200.bed.split6848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6849 0 1 2 100 hg38.150200.bed.split6849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split685 0 1 2 100 hg38.150200.bed.split685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6850 0 1 2 100 hg38.150200.bed.split6850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6851 0 1 2 100 hg38.150200.bed.split6851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6852 0 1 2 100 hg38.150200.bed.split6852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6853 0 1 2 100 hg38.150200.bed.split6853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6854 0 1 2 100 hg38.150200.bed.split6854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6855 0 1 2 100 hg38.150200.bed.split6855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6856 0 1 2 100 hg38.150200.bed.split6856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6857 0 1 2 100 hg38.150200.bed.split6857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6858 0 1 2 100 hg38.150200.bed.split6858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6859 0 1 2 100 hg38.150200.bed.split6859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split686 0 1 2 100 hg38.150200.bed.split686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6860 0 1 2 100 hg38.150200.bed.split6860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6861 0 1 2 100 hg38.150200.bed.split6861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6862 0 1 2 100 hg38.150200.bed.split6862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6863 0 1 2 100 hg38.150200.bed.split6863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6864 0 1 2 100 hg38.150200.bed.split6864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6865 0 1 2 100 hg38.150200.bed.split6865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6866 0 1 2 100 hg38.150200.bed.split6866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6867 0 1 2 100 hg38.150200.bed.split6867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6868 0 1 2 100 hg38.150200.bed.split6868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6869 0 1 2 100 hg38.150200.bed.split6869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split687 0 1 2 100 hg38.150200.bed.split687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6870 0 1 2 100 hg38.150200.bed.split6870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6871 0 1 2 100 hg38.150200.bed.split6871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6872 0 1 2 100 hg38.150200.bed.split6872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6873 0 1 2 100 hg38.150200.bed.split6873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6874 0 1 2 100 hg38.150200.bed.split6874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6875 0 1 2 100 hg38.150200.bed.split6875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6876 0 1 2 100 hg38.150200.bed.split6876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6877 0 1 2 100 hg38.150200.bed.split6877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6878 0 1 2 100 hg38.150200.bed.split6878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6879 0 1 2 100 hg38.150200.bed.split6879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split688 0 1 2 100 hg38.150200.bed.split688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6880 0 1 2 100 hg38.150200.bed.split6880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6881 0 1 2 100 hg38.150200.bed.split6881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6882 0 1 2 100 hg38.150200.bed.split6882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6883 0 1 2 100 hg38.150200.bed.split6883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6884 0 1 2 100 hg38.150200.bed.split6884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6885 0 1 2 100 hg38.150200.bed.split6885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6886 0 1 2 100 hg38.150200.bed.split6886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6887 0 1 2 100 hg38.150200.bed.split6887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6888 0 1 2 100 hg38.150200.bed.split6888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6889 0 1 2 100 hg38.150200.bed.split6889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split689 0 1 2 100 hg38.150200.bed.split689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6890 0 1 2 100 hg38.150200.bed.split6890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6891 0 1 2 100 hg38.150200.bed.split6891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6892 0 1 2 100 hg38.150200.bed.split6892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6893 0 1 2 100 hg38.150200.bed.split6893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6894 0 1 2 100 hg38.150200.bed.split6894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6895 0 1 2 100 hg38.150200.bed.split6895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6896 0 1 2 100 hg38.150200.bed.split6896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6897 0 1 2 100 hg38.150200.bed.split6897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6898 0 1 2 100 hg38.150200.bed.split6898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6899 0 1 2 100 hg38.150200.bed.split6899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split69 0 1 2 100 hg38.150200.bed.split69.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split690 0 1 2 100 hg38.150200.bed.split690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6900 0 1 2 100 hg38.150200.bed.split6900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6901 0 1 2 100 hg38.150200.bed.split6901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6902 0 1 2 100 hg38.150200.bed.split6902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6903 0 1 2 100 hg38.150200.bed.split6903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6904 0 1 2 100 hg38.150200.bed.split6904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6905 0 1 2 100 hg38.150200.bed.split6905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6906 0 1 2 100 hg38.150200.bed.split6906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6907 0 1 2 100 hg38.150200.bed.split6907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6908 0 1 2 100 hg38.150200.bed.split6908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6909 0 1 2 100 hg38.150200.bed.split6909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split691 0 1 2 100 hg38.150200.bed.split691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6910 0 1 2 100 hg38.150200.bed.split6910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6911 0 1 2 100 hg38.150200.bed.split6911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6912 0 1 2 100 hg38.150200.bed.split6912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6913 0 1 2 100 hg38.150200.bed.split6913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6914 0 1 2 100 hg38.150200.bed.split6914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6915 0 1 2 100 hg38.150200.bed.split6915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6916 0 1 2 100 hg38.150200.bed.split6916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6917 0 1 2 100 hg38.150200.bed.split6917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6918 0 1 2 100 hg38.150200.bed.split6918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6919 0 1 2 100 hg38.150200.bed.split6919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split692 0 1 2 100 hg38.150200.bed.split692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6920 0 1 2 100 hg38.150200.bed.split6920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6921 0 1 2 100 hg38.150200.bed.split6921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6922 0 1 2 100 hg38.150200.bed.split6922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6923 0 1 2 100 hg38.150200.bed.split6923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6924 0 1 2 100 hg38.150200.bed.split6924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6925 0 1 2 100 hg38.150200.bed.split6925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6926 0 1 2 100 hg38.150200.bed.split6926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6927 0 1 2 100 hg38.150200.bed.split6927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6928 0 1 2 100 hg38.150200.bed.split6928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6929 0 1 2 100 hg38.150200.bed.split6929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split693 0 1 2 100 hg38.150200.bed.split693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6930 0 1 2 100 hg38.150200.bed.split6930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6931 0 1 2 100 hg38.150200.bed.split6931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6932 0 1 2 100 hg38.150200.bed.split6932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6933 0 1 2 100 hg38.150200.bed.split6933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6934 0 1 2 100 hg38.150200.bed.split6934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6935 0 1 2 100 hg38.150200.bed.split6935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6936 0 1 2 100 hg38.150200.bed.split6936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6937 0 1 2 100 hg38.150200.bed.split6937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6938 0 1 2 100 hg38.150200.bed.split6938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6939 0 1 2 100 hg38.150200.bed.split6939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split694 0 1 2 100 hg38.150200.bed.split694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6940 0 1 2 100 hg38.150200.bed.split6940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6941 0 1 2 100 hg38.150200.bed.split6941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6942 0 1 2 100 hg38.150200.bed.split6942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6943 0 1 2 100 hg38.150200.bed.split6943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6944 0 1 2 100 hg38.150200.bed.split6944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6945 0 1 2 100 hg38.150200.bed.split6945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6946 0 1 2 100 hg38.150200.bed.split6946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6947 0 1 2 100 hg38.150200.bed.split6947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6948 0 1 2 100 hg38.150200.bed.split6948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6949 0 1 2 100 hg38.150200.bed.split6949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split695 0 1 2 100 hg38.150200.bed.split695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6950 0 1 2 100 hg38.150200.bed.split6950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6951 0 1 2 100 hg38.150200.bed.split6951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6952 0 1 2 100 hg38.150200.bed.split6952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6953 0 1 2 100 hg38.150200.bed.split6953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6954 0 1 2 100 hg38.150200.bed.split6954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6955 0 1 2 100 hg38.150200.bed.split6955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6956 0 1 2 100 hg38.150200.bed.split6956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6957 0 1 2 100 hg38.150200.bed.split6957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6958 0 1 2 100 hg38.150200.bed.split6958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6959 0 1 2 100 hg38.150200.bed.split6959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split696 0 1 2 100 hg38.150200.bed.split696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6960 0 1 2 100 hg38.150200.bed.split6960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6961 0 1 2 100 hg38.150200.bed.split6961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6962 0 1 2 100 hg38.150200.bed.split6962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6963 0 1 2 100 hg38.150200.bed.split6963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6964 0 1 2 100 hg38.150200.bed.split6964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6965 0 1 2 100 hg38.150200.bed.split6965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6966 0 1 2 100 hg38.150200.bed.split6966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6967 0 1 2 100 hg38.150200.bed.split6967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6968 0 1 2 100 hg38.150200.bed.split6968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6969 0 1 2 100 hg38.150200.bed.split6969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split697 0 1 2 100 hg38.150200.bed.split697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6970 0 1 2 100 hg38.150200.bed.split6970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6971 0 1 2 100 hg38.150200.bed.split6971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6972 0 1 2 100 hg38.150200.bed.split6972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6973 0 1 2 100 hg38.150200.bed.split6973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6974 0 1 2 100 hg38.150200.bed.split6974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6975 0 1 2 100 hg38.150200.bed.split6975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6976 0 1 2 100 hg38.150200.bed.split6976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6977 0 1 2 100 hg38.150200.bed.split6977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6978 0 1 2 100 hg38.150200.bed.split6978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6979 0 1 2 100 hg38.150200.bed.split6979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split698 0 1 2 100 hg38.150200.bed.split698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6980 0 1 2 100 hg38.150200.bed.split6980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6981 0 1 2 100 hg38.150200.bed.split6981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6982 0 1 2 100 hg38.150200.bed.split6982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6983 0 1 2 100 hg38.150200.bed.split6983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6984 0 1 2 100 hg38.150200.bed.split6984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6985 0 1 2 100 hg38.150200.bed.split6985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6986 0 1 2 100 hg38.150200.bed.split6986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6987 0 1 2 100 hg38.150200.bed.split6987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6988 0 1 2 100 hg38.150200.bed.split6988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6989 0 1 2 100 hg38.150200.bed.split6989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split699 0 1 2 100 hg38.150200.bed.split699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6990 0 1 2 100 hg38.150200.bed.split6990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6991 0 1 2 100 hg38.150200.bed.split6991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6992 0 1 2 100 hg38.150200.bed.split6992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6993 0 1 2 100 hg38.150200.bed.split6993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6994 0 1 2 100 hg38.150200.bed.split6994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6995 0 1 2 100 hg38.150200.bed.split6995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6996 0 1 2 100 hg38.150200.bed.split6996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6997 0 1 2 100 hg38.150200.bed.split6997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6998 0 1 2 100 hg38.150200.bed.split6998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split6999 0 1 2 100 hg38.150200.bed.split6999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7 0 1 2 100 hg38.150200.bed.split7.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split70 0 1 2 100 hg38.150200.bed.split70.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split700 0 1 2 100 hg38.150200.bed.split700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7000 0 1 2 100 hg38.150200.bed.split7000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7001 0 1 2 100 hg38.150200.bed.split7001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7002 0 1 2 100 hg38.150200.bed.split7002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7003 0 1 2 100 hg38.150200.bed.split7003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7004 0 1 2 100 hg38.150200.bed.split7004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7005 0 1 2 100 hg38.150200.bed.split7005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7006 0 1 2 100 hg38.150200.bed.split7006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7007 0 1 2 100 hg38.150200.bed.split7007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7008 0 1 2 100 hg38.150200.bed.split7008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7009 0 1 2 100 hg38.150200.bed.split7009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split701 0 1 2 100 hg38.150200.bed.split701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7010 0 1 2 100 hg38.150200.bed.split7010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7011 0 1 2 100 hg38.150200.bed.split7011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7012 0 1 2 100 hg38.150200.bed.split7012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7013 0 1 2 100 hg38.150200.bed.split7013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7014 0 1 2 100 hg38.150200.bed.split7014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7015 0 1 2 100 hg38.150200.bed.split7015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7016 0 1 2 100 hg38.150200.bed.split7016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7017 0 1 2 100 hg38.150200.bed.split7017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7018 0 1 2 100 hg38.150200.bed.split7018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7019 0 1 2 100 hg38.150200.bed.split7019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split702 0 1 2 100 hg38.150200.bed.split702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7020 0 1 2 100 hg38.150200.bed.split7020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7021 0 1 2 100 hg38.150200.bed.split7021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7022 0 1 2 100 hg38.150200.bed.split7022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7023 0 1 2 100 hg38.150200.bed.split7023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7024 0 1 2 100 hg38.150200.bed.split7024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7025 0 1 2 100 hg38.150200.bed.split7025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7026 0 1 2 100 hg38.150200.bed.split7026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7027 0 1 2 100 hg38.150200.bed.split7027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7028 0 1 2 100 hg38.150200.bed.split7028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7029 0 1 2 100 hg38.150200.bed.split7029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split703 0 1 2 100 hg38.150200.bed.split703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7030 0 1 2 100 hg38.150200.bed.split7030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7031 0 1 2 100 hg38.150200.bed.split7031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7032 0 1 2 100 hg38.150200.bed.split7032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7033 0 1 2 100 hg38.150200.bed.split7033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7034 0 1 2 100 hg38.150200.bed.split7034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7035 0 1 2 100 hg38.150200.bed.split7035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7036 0 1 2 100 hg38.150200.bed.split7036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7037 0 1 2 100 hg38.150200.bed.split7037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7038 0 1 2 100 hg38.150200.bed.split7038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7039 0 1 2 100 hg38.150200.bed.split7039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split704 0 1 2 100 hg38.150200.bed.split704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7040 0 1 2 100 hg38.150200.bed.split7040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7041 0 1 2 100 hg38.150200.bed.split7041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7042 0 1 2 100 hg38.150200.bed.split7042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7043 0 1 2 100 hg38.150200.bed.split7043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7044 0 1 2 100 hg38.150200.bed.split7044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7045 0 1 2 100 hg38.150200.bed.split7045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7046 0 1 2 100 hg38.150200.bed.split7046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7047 0 1 2 100 hg38.150200.bed.split7047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7048 0 1 2 100 hg38.150200.bed.split7048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7049 0 1 2 100 hg38.150200.bed.split7049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split705 0 1 2 100 hg38.150200.bed.split705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7050 0 1 2 100 hg38.150200.bed.split7050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7051 0 1 2 100 hg38.150200.bed.split7051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7052 0 1 2 100 hg38.150200.bed.split7052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7053 0 1 2 100 hg38.150200.bed.split7053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7054 0 1 2 100 hg38.150200.bed.split7054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7055 0 1 2 100 hg38.150200.bed.split7055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7056 0 1 2 100 hg38.150200.bed.split7056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7057 0 1 2 100 hg38.150200.bed.split7057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7058 0 1 2 100 hg38.150200.bed.split7058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7059 0 1 2 100 hg38.150200.bed.split7059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split706 0 1 2 100 hg38.150200.bed.split706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7060 0 1 2 100 hg38.150200.bed.split7060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7061 0 1 2 100 hg38.150200.bed.split7061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7062 0 1 2 100 hg38.150200.bed.split7062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7063 0 1 2 100 hg38.150200.bed.split7063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7064 0 1 2 100 hg38.150200.bed.split7064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7065 0 1 2 100 hg38.150200.bed.split7065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7066 0 1 2 100 hg38.150200.bed.split7066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7067 0 1 2 100 hg38.150200.bed.split7067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7068 0 1 2 100 hg38.150200.bed.split7068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7069 0 1 2 100 hg38.150200.bed.split7069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split707 0 1 2 100 hg38.150200.bed.split707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7070 0 1 2 100 hg38.150200.bed.split7070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7071 0 1 2 100 hg38.150200.bed.split7071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7072 0 1 2 100 hg38.150200.bed.split7072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7073 0 1 2 100 hg38.150200.bed.split7073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7074 0 1 2 100 hg38.150200.bed.split7074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7075 0 1 2 100 hg38.150200.bed.split7075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7076 0 1 2 100 hg38.150200.bed.split7076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7077 0 1 2 100 hg38.150200.bed.split7077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7078 0 1 2 100 hg38.150200.bed.split7078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7079 0 1 2 100 hg38.150200.bed.split7079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split708 0 1 2 100 hg38.150200.bed.split708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7080 0 1 2 100 hg38.150200.bed.split7080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7081 0 1 2 100 hg38.150200.bed.split7081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7082 0 1 2 100 hg38.150200.bed.split7082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7083 0 1 2 100 hg38.150200.bed.split7083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7084 0 1 2 100 hg38.150200.bed.split7084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7085 0 1 2 100 hg38.150200.bed.split7085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7086 0 1 2 100 hg38.150200.bed.split7086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7087 0 1 2 100 hg38.150200.bed.split7087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7088 0 1 2 100 hg38.150200.bed.split7088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7089 0 1 2 100 hg38.150200.bed.split7089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split709 0 1 2 100 hg38.150200.bed.split709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7090 0 1 2 100 hg38.150200.bed.split7090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7091 0 1 2 100 hg38.150200.bed.split7091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7092 0 1 2 100 hg38.150200.bed.split7092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7093 0 1 2 100 hg38.150200.bed.split7093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7094 0 1 2 100 hg38.150200.bed.split7094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7095 0 1 2 100 hg38.150200.bed.split7095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7096 0 1 2 100 hg38.150200.bed.split7096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7097 0 1 2 100 hg38.150200.bed.split7097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7098 0 1 2 100 hg38.150200.bed.split7098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7099 0 1 2 100 hg38.150200.bed.split7099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split71 0 1 2 100 hg38.150200.bed.split71.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split710 0 1 2 100 hg38.150200.bed.split710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7100 0 1 2 100 hg38.150200.bed.split7100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7101 0 1 2 100 hg38.150200.bed.split7101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7102 0 1 2 100 hg38.150200.bed.split7102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7103 0 1 2 100 hg38.150200.bed.split7103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7104 0 1 2 100 hg38.150200.bed.split7104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7105 0 1 2 100 hg38.150200.bed.split7105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7106 0 1 2 100 hg38.150200.bed.split7106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7107 0 1 2 100 hg38.150200.bed.split7107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7108 0 1 2 100 hg38.150200.bed.split7108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7109 0 1 2 100 hg38.150200.bed.split7109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split711 0 1 2 100 hg38.150200.bed.split711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7110 0 1 2 100 hg38.150200.bed.split7110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7111 0 1 2 100 hg38.150200.bed.split7111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7112 0 1 2 100 hg38.150200.bed.split7112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7113 0 1 2 100 hg38.150200.bed.split7113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7114 0 1 2 100 hg38.150200.bed.split7114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7115 0 1 2 100 hg38.150200.bed.split7115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7116 0 1 2 100 hg38.150200.bed.split7116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7117 0 1 2 100 hg38.150200.bed.split7117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7118 0 1 2 100 hg38.150200.bed.split7118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7119 0 1 2 100 hg38.150200.bed.split7119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split712 0 1 2 100 hg38.150200.bed.split712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7120 0 1 2 100 hg38.150200.bed.split7120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7121 0 1 2 100 hg38.150200.bed.split7121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7122 0 1 2 100 hg38.150200.bed.split7122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7123 0 1 2 100 hg38.150200.bed.split7123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7124 0 1 2 100 hg38.150200.bed.split7124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7125 0 1 2 100 hg38.150200.bed.split7125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7126 0 1 2 100 hg38.150200.bed.split7126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7127 0 1 2 100 hg38.150200.bed.split7127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7128 0 1 2 100 hg38.150200.bed.split7128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7129 0 1 2 100 hg38.150200.bed.split7129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split713 0 1 2 100 hg38.150200.bed.split713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7130 0 1 2 100 hg38.150200.bed.split7130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7131 0 1 2 100 hg38.150200.bed.split7131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7132 0 1 2 100 hg38.150200.bed.split7132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7133 0 1 2 100 hg38.150200.bed.split7133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7134 0 1 2 100 hg38.150200.bed.split7134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7135 0 1 2 100 hg38.150200.bed.split7135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7136 0 1 2 100 hg38.150200.bed.split7136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7137 0 1 2 100 hg38.150200.bed.split7137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7138 0 1 2 100 hg38.150200.bed.split7138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7139 0 1 2 100 hg38.150200.bed.split7139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split714 0 1 2 100 hg38.150200.bed.split714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7140 0 1 2 100 hg38.150200.bed.split7140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7141 0 1 2 100 hg38.150200.bed.split7141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7142 0 1 2 100 hg38.150200.bed.split7142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7143 0 1 2 100 hg38.150200.bed.split7143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7144 0 1 2 100 hg38.150200.bed.split7144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7145 0 1 2 100 hg38.150200.bed.split7145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7146 0 1 2 100 hg38.150200.bed.split7146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7147 0 1 2 100 hg38.150200.bed.split7147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7148 0 1 2 100 hg38.150200.bed.split7148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7149 0 1 2 100 hg38.150200.bed.split7149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split715 0 1 2 100 hg38.150200.bed.split715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7150 0 1 2 100 hg38.150200.bed.split7150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7151 0 1 2 100 hg38.150200.bed.split7151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7152 0 1 2 100 hg38.150200.bed.split7152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7153 0 1 2 100 hg38.150200.bed.split7153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7154 0 1 2 100 hg38.150200.bed.split7154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7155 0 1 2 100 hg38.150200.bed.split7155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7156 0 1 2 100 hg38.150200.bed.split7156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7157 0 1 2 100 hg38.150200.bed.split7157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7158 0 1 2 100 hg38.150200.bed.split7158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7159 0 1 2 100 hg38.150200.bed.split7159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split716 0 1 2 100 hg38.150200.bed.split716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7160 0 1 2 100 hg38.150200.bed.split7160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7161 0 1 2 100 hg38.150200.bed.split7161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7162 0 1 2 100 hg38.150200.bed.split7162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7163 0 1 2 100 hg38.150200.bed.split7163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7164 0 1 2 100 hg38.150200.bed.split7164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7165 0 1 2 100 hg38.150200.bed.split7165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7166 0 1 2 100 hg38.150200.bed.split7166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7167 0 1 2 100 hg38.150200.bed.split7167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7168 0 1 2 100 hg38.150200.bed.split7168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7169 0 1 2 100 hg38.150200.bed.split7169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split717 0 1 2 100 hg38.150200.bed.split717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7170 0 1 2 100 hg38.150200.bed.split7170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7171 0 1 2 100 hg38.150200.bed.split7171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7172 0 1 2 100 hg38.150200.bed.split7172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7173 0 1 2 100 hg38.150200.bed.split7173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7174 0 1 2 100 hg38.150200.bed.split7174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7175 0 1 2 100 hg38.150200.bed.split7175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7176 0 1 2 100 hg38.150200.bed.split7176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7177 0 1 2 100 hg38.150200.bed.split7177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7178 0 1 2 100 hg38.150200.bed.split7178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7179 0 1 2 100 hg38.150200.bed.split7179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split718 0 1 2 100 hg38.150200.bed.split718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7180 0 1 2 100 hg38.150200.bed.split7180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7181 0 1 2 100 hg38.150200.bed.split7181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7182 0 1 2 100 hg38.150200.bed.split7182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7183 0 1 2 100 hg38.150200.bed.split7183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7184 0 1 2 100 hg38.150200.bed.split7184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7185 0 1 2 100 hg38.150200.bed.split7185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7186 0 1 2 100 hg38.150200.bed.split7186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7187 0 1 2 100 hg38.150200.bed.split7187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7188 0 1 2 100 hg38.150200.bed.split7188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7189 0 1 2 100 hg38.150200.bed.split7189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split719 0 1 2 100 hg38.150200.bed.split719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7190 0 1 2 100 hg38.150200.bed.split7190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7191 0 1 2 100 hg38.150200.bed.split7191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7192 0 1 2 100 hg38.150200.bed.split7192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7193 0 1 2 100 hg38.150200.bed.split7193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7194 0 1 2 100 hg38.150200.bed.split7194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7195 0 1 2 100 hg38.150200.bed.split7195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7196 0 1 2 100 hg38.150200.bed.split7196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7197 0 1 2 100 hg38.150200.bed.split7197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7198 0 1 2 100 hg38.150200.bed.split7198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7199 0 1 2 100 hg38.150200.bed.split7199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split72 0 1 2 100 hg38.150200.bed.split72.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split720 0 1 2 100 hg38.150200.bed.split720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7200 0 1 2 100 hg38.150200.bed.split7200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7201 0 1 2 100 hg38.150200.bed.split7201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7202 0 1 2 100 hg38.150200.bed.split7202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7203 0 1 2 100 hg38.150200.bed.split7203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7204 0 1 2 100 hg38.150200.bed.split7204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7205 0 1 2 100 hg38.150200.bed.split7205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7206 0 1 2 100 hg38.150200.bed.split7206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7207 0 1 2 100 hg38.150200.bed.split7207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7208 0 1 2 100 hg38.150200.bed.split7208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7209 0 1 2 100 hg38.150200.bed.split7209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split721 0 1 2 100 hg38.150200.bed.split721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7210 0 1 2 100 hg38.150200.bed.split7210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7211 0 1 2 100 hg38.150200.bed.split7211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7212 0 1 2 100 hg38.150200.bed.split7212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7213 0 1 2 100 hg38.150200.bed.split7213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7214 0 1 2 100 hg38.150200.bed.split7214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7215 0 1 2 100 hg38.150200.bed.split7215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7216 0 1 2 100 hg38.150200.bed.split7216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7217 0 1 2 100 hg38.150200.bed.split7217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7218 0 1 2 100 hg38.150200.bed.split7218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7219 0 1 2 100 hg38.150200.bed.split7219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split722 0 1 2 100 hg38.150200.bed.split722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7220 0 1 2 100 hg38.150200.bed.split7220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7221 0 1 2 100 hg38.150200.bed.split7221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7222 0 1 2 100 hg38.150200.bed.split7222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7223 0 1 2 100 hg38.150200.bed.split7223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7224 0 1 2 100 hg38.150200.bed.split7224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7225 0 1 2 100 hg38.150200.bed.split7225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7226 0 1 2 100 hg38.150200.bed.split7226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7227 0 1 2 100 hg38.150200.bed.split7227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7228 0 1 2 100 hg38.150200.bed.split7228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7229 0 1 2 100 hg38.150200.bed.split7229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split723 0 1 2 100 hg38.150200.bed.split723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7230 0 1 2 100 hg38.150200.bed.split7230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7231 0 1 2 100 hg38.150200.bed.split7231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7232 0 1 2 100 hg38.150200.bed.split7232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7233 0 1 2 100 hg38.150200.bed.split7233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7234 0 1 2 100 hg38.150200.bed.split7234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7235 0 1 2 100 hg38.150200.bed.split7235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7236 0 1 2 100 hg38.150200.bed.split7236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7237 0 1 2 100 hg38.150200.bed.split7237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7238 0 1 2 100 hg38.150200.bed.split7238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7239 0 1 2 100 hg38.150200.bed.split7239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split724 0 1 2 100 hg38.150200.bed.split724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7240 0 1 2 100 hg38.150200.bed.split7240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7241 0 1 2 100 hg38.150200.bed.split7241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7242 0 1 2 100 hg38.150200.bed.split7242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7243 0 1 2 100 hg38.150200.bed.split7243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7244 0 1 2 100 hg38.150200.bed.split7244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7245 0 1 2 100 hg38.150200.bed.split7245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7246 0 1 2 100 hg38.150200.bed.split7246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7247 0 1 2 100 hg38.150200.bed.split7247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7248 0 1 2 100 hg38.150200.bed.split7248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7249 0 1 2 100 hg38.150200.bed.split7249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split725 0 1 2 100 hg38.150200.bed.split725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7250 0 1 2 100 hg38.150200.bed.split7250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7251 0 1 2 100 hg38.150200.bed.split7251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7252 0 1 2 100 hg38.150200.bed.split7252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7253 0 1 2 100 hg38.150200.bed.split7253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7254 0 1 2 100 hg38.150200.bed.split7254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7255 0 1 2 100 hg38.150200.bed.split7255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7256 0 1 2 100 hg38.150200.bed.split7256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7257 0 1 2 100 hg38.150200.bed.split7257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7258 0 1 2 100 hg38.150200.bed.split7258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7259 0 1 2 100 hg38.150200.bed.split7259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split726 0 1 2 100 hg38.150200.bed.split726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7260 0 1 2 100 hg38.150200.bed.split7260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7261 0 1 2 100 hg38.150200.bed.split7261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7262 0 1 2 100 hg38.150200.bed.split7262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7263 0 1 2 100 hg38.150200.bed.split7263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7264 0 1 2 100 hg38.150200.bed.split7264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7265 0 1 2 100 hg38.150200.bed.split7265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7266 0 1 2 100 hg38.150200.bed.split7266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7267 0 1 2 100 hg38.150200.bed.split7267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7268 0 1 2 100 hg38.150200.bed.split7268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7269 0 1 2 100 hg38.150200.bed.split7269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split727 0 1 2 100 hg38.150200.bed.split727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7270 0 1 2 100 hg38.150200.bed.split7270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7271 0 1 2 100 hg38.150200.bed.split7271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7272 0 1 2 100 hg38.150200.bed.split7272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7273 0 1 2 100 hg38.150200.bed.split7273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7274 0 1 2 100 hg38.150200.bed.split7274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7275 0 1 2 100 hg38.150200.bed.split7275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7276 0 1 2 100 hg38.150200.bed.split7276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7277 0 1 2 100 hg38.150200.bed.split7277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7278 0 1 2 100 hg38.150200.bed.split7278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7279 0 1 2 100 hg38.150200.bed.split7279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split728 0 1 2 100 hg38.150200.bed.split728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7280 0 1 2 100 hg38.150200.bed.split7280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7281 0 1 2 100 hg38.150200.bed.split7281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7282 0 1 2 100 hg38.150200.bed.split7282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7283 0 1 2 100 hg38.150200.bed.split7283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7284 0 1 2 100 hg38.150200.bed.split7284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7285 0 1 2 100 hg38.150200.bed.split7285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7286 0 1 2 100 hg38.150200.bed.split7286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7287 0 1 2 100 hg38.150200.bed.split7287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7288 0 1 2 100 hg38.150200.bed.split7288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7289 0 1 2 100 hg38.150200.bed.split7289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split729 0 1 2 100 hg38.150200.bed.split729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7290 0 1 2 100 hg38.150200.bed.split7290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7291 0 1 2 100 hg38.150200.bed.split7291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7292 0 1 2 100 hg38.150200.bed.split7292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7293 0 1 2 100 hg38.150200.bed.split7293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7294 0 1 2 100 hg38.150200.bed.split7294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7295 0 1 2 100 hg38.150200.bed.split7295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7296 0 1 2 100 hg38.150200.bed.split7296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7297 0 1 2 100 hg38.150200.bed.split7297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7298 0 1 2 100 hg38.150200.bed.split7298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7299 0 1 2 100 hg38.150200.bed.split7299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split73 0 1 2 100 hg38.150200.bed.split73.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split730 0 1 2 100 hg38.150200.bed.split730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7300 0 1 2 100 hg38.150200.bed.split7300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7301 0 1 2 100 hg38.150200.bed.split7301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7302 0 1 2 100 hg38.150200.bed.split7302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7303 0 1 2 100 hg38.150200.bed.split7303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7304 0 1 2 100 hg38.150200.bed.split7304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7305 0 1 2 100 hg38.150200.bed.split7305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7306 0 1 2 100 hg38.150200.bed.split7306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7307 0 1 2 100 hg38.150200.bed.split7307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7308 0 1 2 100 hg38.150200.bed.split7308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7309 0 1 2 100 hg38.150200.bed.split7309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split731 0 1 2 100 hg38.150200.bed.split731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7310 0 1 2 100 hg38.150200.bed.split7310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7311 0 1 2 100 hg38.150200.bed.split7311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7312 0 1 2 100 hg38.150200.bed.split7312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7313 0 1 2 100 hg38.150200.bed.split7313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7314 0 1 2 100 hg38.150200.bed.split7314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7315 0 1 2 100 hg38.150200.bed.split7315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7316 0 1 2 100 hg38.150200.bed.split7316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7317 0 1 2 100 hg38.150200.bed.split7317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7318 0 1 2 100 hg38.150200.bed.split7318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7319 0 1 2 100 hg38.150200.bed.split7319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split732 0 1 2 100 hg38.150200.bed.split732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7320 0 1 2 100 hg38.150200.bed.split7320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7321 0 1 2 100 hg38.150200.bed.split7321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7322 0 1 2 100 hg38.150200.bed.split7322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7323 0 1 2 100 hg38.150200.bed.split7323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7324 0 1 2 100 hg38.150200.bed.split7324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7325 0 1 2 100 hg38.150200.bed.split7325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7326 0 1 2 100 hg38.150200.bed.split7326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7327 0 1 2 100 hg38.150200.bed.split7327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7328 0 1 2 100 hg38.150200.bed.split7328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7329 0 1 2 100 hg38.150200.bed.split7329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split733 0 1 2 100 hg38.150200.bed.split733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7330 0 1 2 100 hg38.150200.bed.split7330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7331 0 1 2 100 hg38.150200.bed.split7331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7332 0 1 2 100 hg38.150200.bed.split7332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7333 0 1 2 100 hg38.150200.bed.split7333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7334 0 1 2 100 hg38.150200.bed.split7334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7335 0 1 2 100 hg38.150200.bed.split7335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7336 0 1 2 100 hg38.150200.bed.split7336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7337 0 1 2 100 hg38.150200.bed.split7337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7338 0 1 2 100 hg38.150200.bed.split7338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7339 0 1 2 100 hg38.150200.bed.split7339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split734 0 1 2 100 hg38.150200.bed.split734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7340 0 1 2 100 hg38.150200.bed.split7340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7341 0 1 2 100 hg38.150200.bed.split7341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7342 0 1 2 100 hg38.150200.bed.split7342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7343 0 1 2 100 hg38.150200.bed.split7343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7344 0 1 2 100 hg38.150200.bed.split7344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7345 0 1 2 100 hg38.150200.bed.split7345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7346 0 1 2 100 hg38.150200.bed.split7346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7347 0 1 2 100 hg38.150200.bed.split7347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7348 0 1 2 100 hg38.150200.bed.split7348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7349 0 1 2 100 hg38.150200.bed.split7349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split735 0 1 2 100 hg38.150200.bed.split735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7350 0 1 2 100 hg38.150200.bed.split7350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7351 0 1 2 100 hg38.150200.bed.split7351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7352 0 1 2 100 hg38.150200.bed.split7352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7353 0 1 2 100 hg38.150200.bed.split7353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7354 0 1 2 100 hg38.150200.bed.split7354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7355 0 1 2 100 hg38.150200.bed.split7355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7356 0 1 2 100 hg38.150200.bed.split7356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7357 0 1 2 100 hg38.150200.bed.split7357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7358 0 1 2 100 hg38.150200.bed.split7358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7359 0 1 2 100 hg38.150200.bed.split7359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split736 0 1 2 100 hg38.150200.bed.split736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7360 0 1 2 100 hg38.150200.bed.split7360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7361 0 1 2 100 hg38.150200.bed.split7361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7362 0 1 2 100 hg38.150200.bed.split7362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7363 0 1 2 100 hg38.150200.bed.split7363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7364 0 1 2 100 hg38.150200.bed.split7364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7365 0 1 2 100 hg38.150200.bed.split7365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7366 0 1 2 100 hg38.150200.bed.split7366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7367 0 1 2 100 hg38.150200.bed.split7367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7368 0 1 2 100 hg38.150200.bed.split7368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7369 0 1 2 100 hg38.150200.bed.split7369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split737 0 1 2 100 hg38.150200.bed.split737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7370 0 1 2 100 hg38.150200.bed.split7370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7371 0 1 2 100 hg38.150200.bed.split7371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7372 0 1 2 100 hg38.150200.bed.split7372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7373 0 1 2 100 hg38.150200.bed.split7373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7374 0 1 2 100 hg38.150200.bed.split7374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7375 0 1 2 100 hg38.150200.bed.split7375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7376 0 1 2 100 hg38.150200.bed.split7376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7377 0 1 2 100 hg38.150200.bed.split7377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7378 0 1 2 100 hg38.150200.bed.split7378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7379 0 1 2 100 hg38.150200.bed.split7379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split738 0 1 2 100 hg38.150200.bed.split738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7380 0 1 2 100 hg38.150200.bed.split7380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7381 0 1 2 100 hg38.150200.bed.split7381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7382 0 1 2 100 hg38.150200.bed.split7382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7383 0 1 2 100 hg38.150200.bed.split7383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7384 0 1 2 100 hg38.150200.bed.split7384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7385 0 1 2 100 hg38.150200.bed.split7385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7386 0 1 2 100 hg38.150200.bed.split7386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7387 0 1 2 100 hg38.150200.bed.split7387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7388 0 1 2 100 hg38.150200.bed.split7388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7389 0 1 2 100 hg38.150200.bed.split7389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split739 0 1 2 100 hg38.150200.bed.split739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7390 0 1 2 100 hg38.150200.bed.split7390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7391 0 1 2 100 hg38.150200.bed.split7391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7392 0 1 2 100 hg38.150200.bed.split7392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7393 0 1 2 100 hg38.150200.bed.split7393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7394 0 1 2 100 hg38.150200.bed.split7394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7395 0 1 2 100 hg38.150200.bed.split7395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7396 0 1 2 100 hg38.150200.bed.split7396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7397 0 1 2 100 hg38.150200.bed.split7397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7398 0 1 2 100 hg38.150200.bed.split7398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7399 0 1 2 100 hg38.150200.bed.split7399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split74 0 1 2 100 hg38.150200.bed.split74.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split740 0 1 2 100 hg38.150200.bed.split740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7400 0 1 2 100 hg38.150200.bed.split7400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7401 0 1 2 100 hg38.150200.bed.split7401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7402 0 1 2 100 hg38.150200.bed.split7402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7403 0 1 2 100 hg38.150200.bed.split7403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7404 0 1 2 100 hg38.150200.bed.split7404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7405 0 1 2 100 hg38.150200.bed.split7405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7406 0 1 2 100 hg38.150200.bed.split7406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7407 0 1 2 100 hg38.150200.bed.split7407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7408 0 1 2 100 hg38.150200.bed.split7408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7409 0 1 2 100 hg38.150200.bed.split7409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split741 0 1 2 100 hg38.150200.bed.split741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7410 0 1 2 100 hg38.150200.bed.split7410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7411 0 1 2 100 hg38.150200.bed.split7411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7412 0 1 2 100 hg38.150200.bed.split7412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7413 0 1 2 100 hg38.150200.bed.split7413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7414 0 1 2 100 hg38.150200.bed.split7414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7415 0 1 2 100 hg38.150200.bed.split7415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7416 0 1 2 100 hg38.150200.bed.split7416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7417 0 1 2 100 hg38.150200.bed.split7417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7418 0 1 2 100 hg38.150200.bed.split7418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7419 0 1 2 100 hg38.150200.bed.split7419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split742 0 1 2 100 hg38.150200.bed.split742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7420 0 1 2 100 hg38.150200.bed.split7420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7421 0 1 2 100 hg38.150200.bed.split7421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7422 0 1 2 100 hg38.150200.bed.split7422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7423 0 1 2 100 hg38.150200.bed.split7423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7424 0 1 2 100 hg38.150200.bed.split7424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7425 0 1 2 100 hg38.150200.bed.split7425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7426 0 1 2 100 hg38.150200.bed.split7426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7427 0 1 2 100 hg38.150200.bed.split7427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7428 0 1 2 100 hg38.150200.bed.split7428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7429 0 1 2 100 hg38.150200.bed.split7429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split743 0 1 2 100 hg38.150200.bed.split743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7430 0 1 2 100 hg38.150200.bed.split7430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7431 0 1 2 100 hg38.150200.bed.split7431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7432 0 1 2 100 hg38.150200.bed.split7432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7433 0 1 2 100 hg38.150200.bed.split7433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7434 0 1 2 100 hg38.150200.bed.split7434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7435 0 1 2 100 hg38.150200.bed.split7435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7436 0 1 2 100 hg38.150200.bed.split7436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7437 0 1 2 100 hg38.150200.bed.split7437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7438 0 1 2 100 hg38.150200.bed.split7438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7439 0 1 2 100 hg38.150200.bed.split7439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split744 0 1 2 100 hg38.150200.bed.split744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7440 0 1 2 100 hg38.150200.bed.split7440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7441 0 1 2 100 hg38.150200.bed.split7441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7442 0 1 2 100 hg38.150200.bed.split7442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7443 0 1 2 100 hg38.150200.bed.split7443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7444 0 1 2 100 hg38.150200.bed.split7444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7445 0 1 2 100 hg38.150200.bed.split7445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7446 0 1 2 100 hg38.150200.bed.split7446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7447 0 1 2 100 hg38.150200.bed.split7447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7448 0 1 2 100 hg38.150200.bed.split7448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7449 0 1 2 100 hg38.150200.bed.split7449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split745 0 1 2 100 hg38.150200.bed.split745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7450 0 1 2 100 hg38.150200.bed.split7450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7451 0 1 2 100 hg38.150200.bed.split7451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7452 0 1 2 100 hg38.150200.bed.split7452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7453 0 1 2 100 hg38.150200.bed.split7453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7454 0 1 2 100 hg38.150200.bed.split7454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7455 0 1 2 100 hg38.150200.bed.split7455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7456 0 1 2 100 hg38.150200.bed.split7456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7457 0 1 2 100 hg38.150200.bed.split7457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7458 0 1 2 100 hg38.150200.bed.split7458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7459 0 1 2 100 hg38.150200.bed.split7459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split746 0 1 2 100 hg38.150200.bed.split746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7460 0 1 2 100 hg38.150200.bed.split7460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7461 0 1 2 100 hg38.150200.bed.split7461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7462 0 1 2 100 hg38.150200.bed.split7462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7463 0 1 2 100 hg38.150200.bed.split7463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7464 0 1 2 100 hg38.150200.bed.split7464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7465 0 1 2 100 hg38.150200.bed.split7465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7466 0 1 2 100 hg38.150200.bed.split7466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7467 0 1 2 100 hg38.150200.bed.split7467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7468 0 1 2 100 hg38.150200.bed.split7468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7469 0 1 2 100 hg38.150200.bed.split7469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split747 0 1 2 100 hg38.150200.bed.split747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7470 0 1 2 100 hg38.150200.bed.split7470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7471 0 1 2 100 hg38.150200.bed.split7471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7472 0 1 2 100 hg38.150200.bed.split7472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7473 0 1 2 100 hg38.150200.bed.split7473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7474 0 1 2 100 hg38.150200.bed.split7474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7475 0 1 2 100 hg38.150200.bed.split7475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7476 0 1 2 100 hg38.150200.bed.split7476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7477 0 1 2 100 hg38.150200.bed.split7477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7478 0 1 2 100 hg38.150200.bed.split7478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7479 0 1 2 100 hg38.150200.bed.split7479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split748 0 1 2 100 hg38.150200.bed.split748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7480 0 1 2 100 hg38.150200.bed.split7480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7481 0 1 2 100 hg38.150200.bed.split7481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7482 0 1 2 100 hg38.150200.bed.split7482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7483 0 1 2 100 hg38.150200.bed.split7483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7484 0 1 2 100 hg38.150200.bed.split7484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7485 0 1 2 100 hg38.150200.bed.split7485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7486 0 1 2 100 hg38.150200.bed.split7486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7487 0 1 2 100 hg38.150200.bed.split7487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7488 0 1 2 100 hg38.150200.bed.split7488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7489 0 1 2 100 hg38.150200.bed.split7489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split749 0 1 2 100 hg38.150200.bed.split749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7490 0 1 2 100 hg38.150200.bed.split7490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7491 0 1 2 100 hg38.150200.bed.split7491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7492 0 1 2 100 hg38.150200.bed.split7492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7493 0 1 2 100 hg38.150200.bed.split7493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7494 0 1 2 100 hg38.150200.bed.split7494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7495 0 1 2 100 hg38.150200.bed.split7495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7496 0 1 2 100 hg38.150200.bed.split7496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7497 0 1 2 100 hg38.150200.bed.split7497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7498 0 1 2 100 hg38.150200.bed.split7498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7499 0 1 2 100 hg38.150200.bed.split7499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split75 0 1 2 100 hg38.150200.bed.split75.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split750 0 1 2 100 hg38.150200.bed.split750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7500 0 1 2 100 hg38.150200.bed.split7500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7501 0 1 2 100 hg38.150200.bed.split7501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7502 0 1 2 100 hg38.150200.bed.split7502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7503 0 1 2 100 hg38.150200.bed.split7503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7504 0 1 2 100 hg38.150200.bed.split7504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7505 0 1 2 100 hg38.150200.bed.split7505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7506 0 1 2 100 hg38.150200.bed.split7506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7507 0 1 2 100 hg38.150200.bed.split7507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7508 0 1 2 100 hg38.150200.bed.split7508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7509 0 1 2 100 hg38.150200.bed.split7509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split751 0 1 2 100 hg38.150200.bed.split751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7510 0 1 2 100 hg38.150200.bed.split7510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7511 0 1 2 100 hg38.150200.bed.split7511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7512 0 1 2 100 hg38.150200.bed.split7512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7513 0 1 2 100 hg38.150200.bed.split7513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7514 0 1 2 100 hg38.150200.bed.split7514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7515 0 1 2 100 hg38.150200.bed.split7515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7516 0 1 2 100 hg38.150200.bed.split7516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7517 0 1 2 100 hg38.150200.bed.split7517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7518 0 1 2 100 hg38.150200.bed.split7518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7519 0 1 2 100 hg38.150200.bed.split7519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split752 0 1 2 100 hg38.150200.bed.split752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7520 0 1 2 100 hg38.150200.bed.split7520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7521 0 1 2 100 hg38.150200.bed.split7521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7522 0 1 2 100 hg38.150200.bed.split7522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7523 0 1 2 100 hg38.150200.bed.split7523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7524 0 1 2 100 hg38.150200.bed.split7524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7525 0 1 2 100 hg38.150200.bed.split7525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7526 0 1 2 100 hg38.150200.bed.split7526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7527 0 1 2 100 hg38.150200.bed.split7527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7528 0 1 2 100 hg38.150200.bed.split7528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7529 0 1 2 100 hg38.150200.bed.split7529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split753 0 1 2 100 hg38.150200.bed.split753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7530 0 1 2 100 hg38.150200.bed.split7530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7531 0 1 2 100 hg38.150200.bed.split7531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7532 0 1 2 100 hg38.150200.bed.split7532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7533 0 1 2 100 hg38.150200.bed.split7533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7534 0 1 2 100 hg38.150200.bed.split7534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7535 0 1 2 100 hg38.150200.bed.split7535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7536 0 1 2 100 hg38.150200.bed.split7536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7537 0 1 2 100 hg38.150200.bed.split7537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7538 0 1 2 100 hg38.150200.bed.split7538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7539 0 1 2 100 hg38.150200.bed.split7539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split754 0 1 2 100 hg38.150200.bed.split754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7540 0 1 2 100 hg38.150200.bed.split7540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7541 0 1 2 100 hg38.150200.bed.split7541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7542 0 1 2 100 hg38.150200.bed.split7542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7543 0 1 2 100 hg38.150200.bed.split7543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7544 0 1 2 100 hg38.150200.bed.split7544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7545 0 1 2 100 hg38.150200.bed.split7545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7546 0 1 2 100 hg38.150200.bed.split7546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7547 0 1 2 100 hg38.150200.bed.split7547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7548 0 1 2 100 hg38.150200.bed.split7548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7549 0 1 2 100 hg38.150200.bed.split7549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split755 0 1 2 100 hg38.150200.bed.split755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7550 0 1 2 100 hg38.150200.bed.split7550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7551 0 1 2 100 hg38.150200.bed.split7551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7552 0 1 2 100 hg38.150200.bed.split7552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7553 0 1 2 100 hg38.150200.bed.split7553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7554 0 1 2 100 hg38.150200.bed.split7554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7555 0 1 2 100 hg38.150200.bed.split7555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7556 0 1 2 100 hg38.150200.bed.split7556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7557 0 1 2 100 hg38.150200.bed.split7557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7558 0 1 2 100 hg38.150200.bed.split7558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7559 0 1 2 100 hg38.150200.bed.split7559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split756 0 1 2 100 hg38.150200.bed.split756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7560 0 1 2 100 hg38.150200.bed.split7560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7561 0 1 2 100 hg38.150200.bed.split7561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7562 0 1 2 100 hg38.150200.bed.split7562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7563 0 1 2 100 hg38.150200.bed.split7563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7564 0 1 2 100 hg38.150200.bed.split7564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7565 0 1 2 100 hg38.150200.bed.split7565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7566 0 1 2 100 hg38.150200.bed.split7566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7567 0 1 2 100 hg38.150200.bed.split7567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7568 0 1 2 100 hg38.150200.bed.split7568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7569 0 1 2 100 hg38.150200.bed.split7569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split757 0 1 2 100 hg38.150200.bed.split757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7570 0 1 2 100 hg38.150200.bed.split7570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7571 0 1 2 100 hg38.150200.bed.split7571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7572 0 1 2 100 hg38.150200.bed.split7572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7573 0 1 2 100 hg38.150200.bed.split7573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7574 0 1 2 100 hg38.150200.bed.split7574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7575 0 1 2 100 hg38.150200.bed.split7575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7576 0 1 2 100 hg38.150200.bed.split7576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7577 0 1 2 100 hg38.150200.bed.split7577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7578 0 1 2 100 hg38.150200.bed.split7578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7579 0 1 2 100 hg38.150200.bed.split7579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split758 0 1 2 100 hg38.150200.bed.split758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7580 0 1 2 100 hg38.150200.bed.split7580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7581 0 1 2 100 hg38.150200.bed.split7581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7582 0 1 2 100 hg38.150200.bed.split7582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7583 0 1 2 100 hg38.150200.bed.split7583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7584 0 1 2 100 hg38.150200.bed.split7584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7585 0 1 2 100 hg38.150200.bed.split7585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7586 0 1 2 100 hg38.150200.bed.split7586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7587 0 1 2 100 hg38.150200.bed.split7587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7588 0 1 2 100 hg38.150200.bed.split7588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7589 0 1 2 100 hg38.150200.bed.split7589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split759 0 1 2 100 hg38.150200.bed.split759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7590 0 1 2 100 hg38.150200.bed.split7590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7591 0 1 2 100 hg38.150200.bed.split7591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7592 0 1 2 100 hg38.150200.bed.split7592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7593 0 1 2 100 hg38.150200.bed.split7593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7594 0 1 2 100 hg38.150200.bed.split7594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7595 0 1 2 100 hg38.150200.bed.split7595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7596 0 1 2 100 hg38.150200.bed.split7596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7597 0 1 2 100 hg38.150200.bed.split7597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7598 0 1 2 100 hg38.150200.bed.split7598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7599 0 1 2 100 hg38.150200.bed.split7599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split76 0 1 2 100 hg38.150200.bed.split76.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split760 0 1 2 100 hg38.150200.bed.split760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7600 0 1 2 100 hg38.150200.bed.split7600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7601 0 1 2 100 hg38.150200.bed.split7601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7602 0 1 2 100 hg38.150200.bed.split7602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7603 0 1 2 100 hg38.150200.bed.split7603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7604 0 1 2 100 hg38.150200.bed.split7604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7605 0 1 2 100 hg38.150200.bed.split7605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7606 0 1 2 100 hg38.150200.bed.split7606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7607 0 1 2 100 hg38.150200.bed.split7607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7608 0 1 2 100 hg38.150200.bed.split7608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7609 0 1 2 100 hg38.150200.bed.split7609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split761 0 1 2 100 hg38.150200.bed.split761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7610 0 1 2 100 hg38.150200.bed.split7610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7611 0 1 2 100 hg38.150200.bed.split7611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7612 0 1 2 100 hg38.150200.bed.split7612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7613 0 1 2 100 hg38.150200.bed.split7613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7614 0 1 2 100 hg38.150200.bed.split7614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7615 0 1 2 100 hg38.150200.bed.split7615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7616 0 1 2 100 hg38.150200.bed.split7616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7617 0 1 2 100 hg38.150200.bed.split7617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7618 0 1 2 100 hg38.150200.bed.split7618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7619 0 1 2 100 hg38.150200.bed.split7619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split762 0 1 2 100 hg38.150200.bed.split762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7620 0 1 2 100 hg38.150200.bed.split7620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7621 0 1 2 100 hg38.150200.bed.split7621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7622 0 1 2 100 hg38.150200.bed.split7622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7623 0 1 2 100 hg38.150200.bed.split7623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7624 0 1 2 100 hg38.150200.bed.split7624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7625 0 1 2 100 hg38.150200.bed.split7625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7626 0 1 2 100 hg38.150200.bed.split7626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7627 0 1 2 100 hg38.150200.bed.split7627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7628 0 1 2 100 hg38.150200.bed.split7628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7629 0 1 2 100 hg38.150200.bed.split7629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split763 0 1 2 100 hg38.150200.bed.split763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7630 0 1 2 100 hg38.150200.bed.split7630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7631 0 1 2 100 hg38.150200.bed.split7631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7632 0 1 2 100 hg38.150200.bed.split7632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7633 0 1 2 100 hg38.150200.bed.split7633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7634 0 1 2 100 hg38.150200.bed.split7634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7635 0 1 2 100 hg38.150200.bed.split7635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7636 0 1 2 100 hg38.150200.bed.split7636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7637 0 1 2 100 hg38.150200.bed.split7637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7638 0 1 2 100 hg38.150200.bed.split7638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7639 0 1 2 100 hg38.150200.bed.split7639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split764 0 1 2 100 hg38.150200.bed.split764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7640 0 1 2 100 hg38.150200.bed.split7640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7641 0 1 2 100 hg38.150200.bed.split7641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7642 0 1 2 100 hg38.150200.bed.split7642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7643 0 1 2 100 hg38.150200.bed.split7643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7644 0 1 2 100 hg38.150200.bed.split7644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7645 0 1 2 100 hg38.150200.bed.split7645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7646 0 1 2 100 hg38.150200.bed.split7646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7647 0 1 2 100 hg38.150200.bed.split7647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7648 0 1 2 100 hg38.150200.bed.split7648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7649 0 1 2 100 hg38.150200.bed.split7649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split765 0 1 2 100 hg38.150200.bed.split765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7650 0 1 2 100 hg38.150200.bed.split7650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7651 0 1 2 100 hg38.150200.bed.split7651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7652 0 1 2 100 hg38.150200.bed.split7652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7653 0 1 2 100 hg38.150200.bed.split7653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7654 0 1 2 100 hg38.150200.bed.split7654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7655 0 1 2 100 hg38.150200.bed.split7655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7656 0 1 2 100 hg38.150200.bed.split7656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7657 0 1 2 100 hg38.150200.bed.split7657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7658 0 1 2 100 hg38.150200.bed.split7658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7659 0 1 2 100 hg38.150200.bed.split7659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split766 0 1 2 100 hg38.150200.bed.split766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7660 0 1 2 100 hg38.150200.bed.split7660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7661 0 1 2 100 hg38.150200.bed.split7661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7662 0 1 2 100 hg38.150200.bed.split7662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7663 0 1 2 100 hg38.150200.bed.split7663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7664 0 1 2 100 hg38.150200.bed.split7664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7665 0 1 2 100 hg38.150200.bed.split7665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7666 0 1 2 100 hg38.150200.bed.split7666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7667 0 1 2 100 hg38.150200.bed.split7667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7668 0 1 2 100 hg38.150200.bed.split7668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7669 0 1 2 100 hg38.150200.bed.split7669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split767 0 1 2 100 hg38.150200.bed.split767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7670 0 1 2 100 hg38.150200.bed.split7670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7671 0 1 2 100 hg38.150200.bed.split7671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7672 0 1 2 100 hg38.150200.bed.split7672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7673 0 1 2 100 hg38.150200.bed.split7673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7674 0 1 2 100 hg38.150200.bed.split7674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7675 0 1 2 100 hg38.150200.bed.split7675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7676 0 1 2 100 hg38.150200.bed.split7676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7677 0 1 2 100 hg38.150200.bed.split7677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7678 0 1 2 100 hg38.150200.bed.split7678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7679 0 1 2 100 hg38.150200.bed.split7679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split768 0 1 2 100 hg38.150200.bed.split768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7680 0 1 2 100 hg38.150200.bed.split7680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7681 0 1 2 100 hg38.150200.bed.split7681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7682 0 1 2 100 hg38.150200.bed.split7682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7683 0 1 2 100 hg38.150200.bed.split7683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7684 0 1 2 100 hg38.150200.bed.split7684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7685 0 1 2 100 hg38.150200.bed.split7685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7686 0 1 2 100 hg38.150200.bed.split7686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7687 0 1 2 100 hg38.150200.bed.split7687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7688 0 1 2 100 hg38.150200.bed.split7688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7689 0 1 2 100 hg38.150200.bed.split7689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split769 0 1 2 100 hg38.150200.bed.split769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7690 0 1 2 100 hg38.150200.bed.split7690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7691 0 1 2 100 hg38.150200.bed.split7691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7692 0 1 2 100 hg38.150200.bed.split7692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7693 0 1 2 100 hg38.150200.bed.split7693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7694 0 1 2 100 hg38.150200.bed.split7694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7695 0 1 2 100 hg38.150200.bed.split7695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7696 0 1 2 100 hg38.150200.bed.split7696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7697 0 1 2 100 hg38.150200.bed.split7697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7698 0 1 2 100 hg38.150200.bed.split7698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7699 0 1 2 100 hg38.150200.bed.split7699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split77 0 1 2 100 hg38.150200.bed.split77.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split770 0 1 2 100 hg38.150200.bed.split770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7700 0 1 2 100 hg38.150200.bed.split7700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7701 0 1 2 100 hg38.150200.bed.split7701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7702 0 1 2 100 hg38.150200.bed.split7702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7703 0 1 2 100 hg38.150200.bed.split7703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7704 0 1 2 100 hg38.150200.bed.split7704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7705 0 1 2 100 hg38.150200.bed.split7705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7706 0 1 2 100 hg38.150200.bed.split7706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7707 0 1 2 100 hg38.150200.bed.split7707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7708 0 1 2 100 hg38.150200.bed.split7708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7709 0 1 2 100 hg38.150200.bed.split7709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split771 0 1 2 100 hg38.150200.bed.split771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7710 0 1 2 100 hg38.150200.bed.split7710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7711 0 1 2 100 hg38.150200.bed.split7711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7712 0 1 2 100 hg38.150200.bed.split7712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7713 0 1 2 100 hg38.150200.bed.split7713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7714 0 1 2 100 hg38.150200.bed.split7714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7715 0 1 2 100 hg38.150200.bed.split7715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7716 0 1 2 100 hg38.150200.bed.split7716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7717 0 1 2 100 hg38.150200.bed.split7717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7718 0 1 2 100 hg38.150200.bed.split7718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7719 0 1 2 100 hg38.150200.bed.split7719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split772 0 1 2 100 hg38.150200.bed.split772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7720 0 1 2 100 hg38.150200.bed.split7720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7721 0 1 2 100 hg38.150200.bed.split7721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7722 0 1 2 100 hg38.150200.bed.split7722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7723 0 1 2 100 hg38.150200.bed.split7723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7724 0 1 2 100 hg38.150200.bed.split7724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7725 0 1 2 100 hg38.150200.bed.split7725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7726 0 1 2 100 hg38.150200.bed.split7726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7727 0 1 2 100 hg38.150200.bed.split7727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7728 0 1 2 100 hg38.150200.bed.split7728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7729 0 1 2 100 hg38.150200.bed.split7729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split773 0 1 2 100 hg38.150200.bed.split773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7730 0 1 2 100 hg38.150200.bed.split7730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7731 0 1 2 100 hg38.150200.bed.split7731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7732 0 1 2 100 hg38.150200.bed.split7732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7733 0 1 2 100 hg38.150200.bed.split7733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7734 0 1 2 100 hg38.150200.bed.split7734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7735 0 1 2 100 hg38.150200.bed.split7735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7736 0 1 2 100 hg38.150200.bed.split7736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7737 0 1 2 100 hg38.150200.bed.split7737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7738 0 1 2 100 hg38.150200.bed.split7738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7739 0 1 2 100 hg38.150200.bed.split7739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split774 0 1 2 100 hg38.150200.bed.split774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7740 0 1 2 100 hg38.150200.bed.split7740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7741 0 1 2 100 hg38.150200.bed.split7741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7742 0 1 2 100 hg38.150200.bed.split7742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7743 0 1 2 100 hg38.150200.bed.split7743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7744 0 1 2 100 hg38.150200.bed.split7744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7745 0 1 2 100 hg38.150200.bed.split7745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7746 0 1 2 100 hg38.150200.bed.split7746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7747 0 1 2 100 hg38.150200.bed.split7747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7748 0 1 2 100 hg38.150200.bed.split7748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7749 0 1 2 100 hg38.150200.bed.split7749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split775 0 1 2 100 hg38.150200.bed.split775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7750 0 1 2 100 hg38.150200.bed.split7750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7751 0 1 2 100 hg38.150200.bed.split7751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7752 0 1 2 100 hg38.150200.bed.split7752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7753 0 1 2 100 hg38.150200.bed.split7753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7754 0 1 2 100 hg38.150200.bed.split7754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7755 0 1 2 100 hg38.150200.bed.split7755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7756 0 1 2 100 hg38.150200.bed.split7756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7757 0 1 2 100 hg38.150200.bed.split7757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7758 0 1 2 100 hg38.150200.bed.split7758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7759 0 1 2 100 hg38.150200.bed.split7759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split776 0 1 2 100 hg38.150200.bed.split776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7760 0 1 2 100 hg38.150200.bed.split7760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7761 0 1 2 100 hg38.150200.bed.split7761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7762 0 1 2 100 hg38.150200.bed.split7762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7763 0 1 2 100 hg38.150200.bed.split7763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7764 0 1 2 100 hg38.150200.bed.split7764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7765 0 1 2 100 hg38.150200.bed.split7765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7766 0 1 2 100 hg38.150200.bed.split7766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7767 0 1 2 100 hg38.150200.bed.split7767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7768 0 1 2 100 hg38.150200.bed.split7768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7769 0 1 2 100 hg38.150200.bed.split7769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split777 0 1 2 100 hg38.150200.bed.split777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7770 0 1 2 100 hg38.150200.bed.split7770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7771 0 1 2 100 hg38.150200.bed.split7771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7772 0 1 2 100 hg38.150200.bed.split7772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7773 0 1 2 100 hg38.150200.bed.split7773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7774 0 1 2 100 hg38.150200.bed.split7774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7775 0 1 2 100 hg38.150200.bed.split7775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7776 0 1 2 100 hg38.150200.bed.split7776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7777 0 1 2 100 hg38.150200.bed.split7777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7778 0 1 2 100 hg38.150200.bed.split7778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7779 0 1 2 100 hg38.150200.bed.split7779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split778 0 1 2 100 hg38.150200.bed.split778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7780 0 1 2 100 hg38.150200.bed.split7780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7781 0 1 2 100 hg38.150200.bed.split7781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7782 0 1 2 100 hg38.150200.bed.split7782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7783 0 1 2 100 hg38.150200.bed.split7783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7784 0 1 2 100 hg38.150200.bed.split7784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7785 0 1 2 100 hg38.150200.bed.split7785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7786 0 1 2 100 hg38.150200.bed.split7786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7787 0 1 2 100 hg38.150200.bed.split7787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7788 0 1 2 100 hg38.150200.bed.split7788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7789 0 1 2 100 hg38.150200.bed.split7789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split779 0 1 2 100 hg38.150200.bed.split779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7790 0 1 2 100 hg38.150200.bed.split7790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7791 0 1 2 100 hg38.150200.bed.split7791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7792 0 1 2 100 hg38.150200.bed.split7792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7793 0 1 2 100 hg38.150200.bed.split7793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7794 0 1 2 100 hg38.150200.bed.split7794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7795 0 1 2 100 hg38.150200.bed.split7795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7796 0 1 2 100 hg38.150200.bed.split7796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7797 0 1 2 100 hg38.150200.bed.split7797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7798 0 1 2 100 hg38.150200.bed.split7798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7799 0 1 2 100 hg38.150200.bed.split7799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split78 0 1 2 100 hg38.150200.bed.split78.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split780 0 1 2 100 hg38.150200.bed.split780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7800 0 1 2 100 hg38.150200.bed.split7800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7801 0 1 2 100 hg38.150200.bed.split7801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7802 0 1 2 100 hg38.150200.bed.split7802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7803 0 1 2 100 hg38.150200.bed.split7803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7804 0 1 2 100 hg38.150200.bed.split7804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7805 0 1 2 100 hg38.150200.bed.split7805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7806 0 1 2 100 hg38.150200.bed.split7806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7807 0 1 2 100 hg38.150200.bed.split7807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7808 0 1 2 100 hg38.150200.bed.split7808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7809 0 1 2 100 hg38.150200.bed.split7809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split781 0 1 2 100 hg38.150200.bed.split781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7810 0 1 2 100 hg38.150200.bed.split7810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7811 0 1 2 100 hg38.150200.bed.split7811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7812 0 1 2 100 hg38.150200.bed.split7812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7813 0 1 2 100 hg38.150200.bed.split7813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7814 0 1 2 100 hg38.150200.bed.split7814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7815 0 1 2 100 hg38.150200.bed.split7815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7816 0 1 2 100 hg38.150200.bed.split7816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7817 0 1 2 100 hg38.150200.bed.split7817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7818 0 1 2 100 hg38.150200.bed.split7818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7819 0 1 2 100 hg38.150200.bed.split7819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split782 0 1 2 100 hg38.150200.bed.split782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7820 0 1 2 100 hg38.150200.bed.split7820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7821 0 1 2 100 hg38.150200.bed.split7821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7822 0 1 2 100 hg38.150200.bed.split7822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7823 0 1 2 100 hg38.150200.bed.split7823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7824 0 1 2 100 hg38.150200.bed.split7824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7825 0 1 2 100 hg38.150200.bed.split7825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7826 0 1 2 100 hg38.150200.bed.split7826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7827 0 1 2 100 hg38.150200.bed.split7827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7828 0 1 2 100 hg38.150200.bed.split7828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7829 0 1 2 100 hg38.150200.bed.split7829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split783 0 1 2 100 hg38.150200.bed.split783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7830 0 1 2 100 hg38.150200.bed.split7830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7831 0 1 2 100 hg38.150200.bed.split7831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7832 0 1 2 100 hg38.150200.bed.split7832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7833 0 1 2 100 hg38.150200.bed.split7833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7834 0 1 2 100 hg38.150200.bed.split7834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7835 0 1 2 100 hg38.150200.bed.split7835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7836 0 1 2 100 hg38.150200.bed.split7836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7837 0 1 2 100 hg38.150200.bed.split7837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7838 0 1 2 100 hg38.150200.bed.split7838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7839 0 1 2 100 hg38.150200.bed.split7839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split784 0 1 2 100 hg38.150200.bed.split784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7840 0 1 2 100 hg38.150200.bed.split7840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7841 0 1 2 100 hg38.150200.bed.split7841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7842 0 1 2 100 hg38.150200.bed.split7842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7843 0 1 2 100 hg38.150200.bed.split7843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7844 0 1 2 100 hg38.150200.bed.split7844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7845 0 1 2 100 hg38.150200.bed.split7845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7846 0 1 2 100 hg38.150200.bed.split7846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7847 0 1 2 100 hg38.150200.bed.split7847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7848 0 1 2 100 hg38.150200.bed.split7848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7849 0 1 2 100 hg38.150200.bed.split7849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split785 0 1 2 100 hg38.150200.bed.split785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7850 0 1 2 100 hg38.150200.bed.split7850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7851 0 1 2 100 hg38.150200.bed.split7851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7852 0 1 2 100 hg38.150200.bed.split7852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7853 0 1 2 100 hg38.150200.bed.split7853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7854 0 1 2 100 hg38.150200.bed.split7854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7855 0 1 2 100 hg38.150200.bed.split7855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7856 0 1 2 100 hg38.150200.bed.split7856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7857 0 1 2 100 hg38.150200.bed.split7857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7858 0 1 2 100 hg38.150200.bed.split7858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7859 0 1 2 100 hg38.150200.bed.split7859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split786 0 1 2 100 hg38.150200.bed.split786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7860 0 1 2 100 hg38.150200.bed.split7860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7861 0 1 2 100 hg38.150200.bed.split7861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7862 0 1 2 100 hg38.150200.bed.split7862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7863 0 1 2 100 hg38.150200.bed.split7863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7864 0 1 2 100 hg38.150200.bed.split7864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7865 0 1 2 100 hg38.150200.bed.split7865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7866 0 1 2 100 hg38.150200.bed.split7866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7867 0 1 2 100 hg38.150200.bed.split7867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7868 0 1 2 100 hg38.150200.bed.split7868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7869 0 1 2 100 hg38.150200.bed.split7869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split787 0 1 2 100 hg38.150200.bed.split787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7870 0 1 2 100 hg38.150200.bed.split7870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7871 0 1 2 100 hg38.150200.bed.split7871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7872 0 1 2 100 hg38.150200.bed.split7872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7873 0 1 2 100 hg38.150200.bed.split7873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7874 0 1 2 100 hg38.150200.bed.split7874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7875 0 1 2 100 hg38.150200.bed.split7875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7876 0 1 2 100 hg38.150200.bed.split7876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7877 0 1 2 100 hg38.150200.bed.split7877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7878 0 1 2 100 hg38.150200.bed.split7878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7879 0 1 2 100 hg38.150200.bed.split7879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split788 0 1 2 100 hg38.150200.bed.split788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7880 0 1 2 100 hg38.150200.bed.split7880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7881 0 1 2 100 hg38.150200.bed.split7881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7882 0 1 2 100 hg38.150200.bed.split7882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7883 0 1 2 100 hg38.150200.bed.split7883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7884 0 1 2 100 hg38.150200.bed.split7884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7885 0 1 2 100 hg38.150200.bed.split7885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7886 0 1 2 100 hg38.150200.bed.split7886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7887 0 1 2 100 hg38.150200.bed.split7887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7888 0 1 2 100 hg38.150200.bed.split7888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7889 0 1 2 100 hg38.150200.bed.split7889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split789 0 1 2 100 hg38.150200.bed.split789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7890 0 1 2 100 hg38.150200.bed.split7890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7891 0 1 2 100 hg38.150200.bed.split7891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7892 0 1 2 100 hg38.150200.bed.split7892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7893 0 1 2 100 hg38.150200.bed.split7893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7894 0 1 2 100 hg38.150200.bed.split7894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7895 0 1 2 100 hg38.150200.bed.split7895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7896 0 1 2 100 hg38.150200.bed.split7896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7897 0 1 2 100 hg38.150200.bed.split7897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7898 0 1 2 100 hg38.150200.bed.split7898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7899 0 1 2 100 hg38.150200.bed.split7899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split79 0 1 2 100 hg38.150200.bed.split79.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split790 0 1 2 100 hg38.150200.bed.split790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7900 0 1 2 100 hg38.150200.bed.split7900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7901 0 1 2 100 hg38.150200.bed.split7901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7902 0 1 2 100 hg38.150200.bed.split7902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7903 0 1 2 100 hg38.150200.bed.split7903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7904 0 1 2 100 hg38.150200.bed.split7904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7905 0 1 2 100 hg38.150200.bed.split7905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7906 0 1 2 100 hg38.150200.bed.split7906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7907 0 1 2 100 hg38.150200.bed.split7907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7908 0 1 2 100 hg38.150200.bed.split7908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7909 0 1 2 100 hg38.150200.bed.split7909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split791 0 1 2 100 hg38.150200.bed.split791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7910 0 1 2 100 hg38.150200.bed.split7910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7911 0 1 2 100 hg38.150200.bed.split7911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7912 0 1 2 100 hg38.150200.bed.split7912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7913 0 1 2 100 hg38.150200.bed.split7913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7914 0 1 2 100 hg38.150200.bed.split7914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7915 0 1 2 100 hg38.150200.bed.split7915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7916 0 1 2 100 hg38.150200.bed.split7916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7917 0 1 2 100 hg38.150200.bed.split7917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7918 0 1 2 100 hg38.150200.bed.split7918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7919 0 1 2 100 hg38.150200.bed.split7919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split792 0 1 2 100 hg38.150200.bed.split792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7920 0 1 2 100 hg38.150200.bed.split7920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7921 0 1 2 100 hg38.150200.bed.split7921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7922 0 1 2 100 hg38.150200.bed.split7922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7923 0 1 2 100 hg38.150200.bed.split7923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7924 0 1 2 100 hg38.150200.bed.split7924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7925 0 1 2 100 hg38.150200.bed.split7925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7926 0 1 2 100 hg38.150200.bed.split7926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7927 0 1 2 100 hg38.150200.bed.split7927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7928 0 1 2 100 hg38.150200.bed.split7928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7929 0 1 2 100 hg38.150200.bed.split7929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split793 0 1 2 100 hg38.150200.bed.split793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7930 0 1 2 100 hg38.150200.bed.split7930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7931 0 1 2 100 hg38.150200.bed.split7931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7932 0 1 2 100 hg38.150200.bed.split7932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7933 0 1 2 100 hg38.150200.bed.split7933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7934 0 1 2 100 hg38.150200.bed.split7934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7935 0 1 2 100 hg38.150200.bed.split7935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7936 0 1 2 100 hg38.150200.bed.split7936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7937 0 1 2 100 hg38.150200.bed.split7937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7938 0 1 2 100 hg38.150200.bed.split7938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7939 0 1 2 100 hg38.150200.bed.split7939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split794 0 1 2 100 hg38.150200.bed.split794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7940 0 1 2 100 hg38.150200.bed.split7940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7941 0 1 2 100 hg38.150200.bed.split7941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7942 0 1 2 100 hg38.150200.bed.split7942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7943 0 1 2 100 hg38.150200.bed.split7943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7944 0 1 2 100 hg38.150200.bed.split7944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7945 0 1 2 100 hg38.150200.bed.split7945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7946 0 1 2 100 hg38.150200.bed.split7946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7947 0 1 2 100 hg38.150200.bed.split7947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7948 0 1 2 100 hg38.150200.bed.split7948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7949 0 1 2 100 hg38.150200.bed.split7949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split795 0 1 2 100 hg38.150200.bed.split795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7950 0 1 2 100 hg38.150200.bed.split7950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7951 0 1 2 100 hg38.150200.bed.split7951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7952 0 1 2 100 hg38.150200.bed.split7952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7953 0 1 2 100 hg38.150200.bed.split7953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7954 0 1 2 100 hg38.150200.bed.split7954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7955 0 1 2 100 hg38.150200.bed.split7955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7956 0 1 2 100 hg38.150200.bed.split7956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7957 0 1 2 100 hg38.150200.bed.split7957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7958 0 1 2 100 hg38.150200.bed.split7958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7959 0 1 2 100 hg38.150200.bed.split7959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split796 0 1 2 100 hg38.150200.bed.split796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7960 0 1 2 100 hg38.150200.bed.split7960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7961 0 1 2 100 hg38.150200.bed.split7961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7962 0 1 2 100 hg38.150200.bed.split7962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7963 0 1 2 100 hg38.150200.bed.split7963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7964 0 1 2 100 hg38.150200.bed.split7964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7965 0 1 2 100 hg38.150200.bed.split7965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7966 0 1 2 100 hg38.150200.bed.split7966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7967 0 1 2 100 hg38.150200.bed.split7967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7968 0 1 2 100 hg38.150200.bed.split7968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7969 0 1 2 100 hg38.150200.bed.split7969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split797 0 1 2 100 hg38.150200.bed.split797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7970 0 1 2 100 hg38.150200.bed.split7970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7971 0 1 2 100 hg38.150200.bed.split7971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7972 0 1 2 100 hg38.150200.bed.split7972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7973 0 1 2 100 hg38.150200.bed.split7973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7974 0 1 2 100 hg38.150200.bed.split7974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7975 0 1 2 100 hg38.150200.bed.split7975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7976 0 1 2 100 hg38.150200.bed.split7976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7977 0 1 2 100 hg38.150200.bed.split7977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7978 0 1 2 100 hg38.150200.bed.split7978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7979 0 1 2 100 hg38.150200.bed.split7979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split798 0 1 2 100 hg38.150200.bed.split798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7980 0 1 2 100 hg38.150200.bed.split7980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7981 0 1 2 100 hg38.150200.bed.split7981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7982 0 1 2 100 hg38.150200.bed.split7982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7983 0 1 2 100 hg38.150200.bed.split7983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7984 0 1 2 100 hg38.150200.bed.split7984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7985 0 1 2 100 hg38.150200.bed.split7985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7986 0 1 2 100 hg38.150200.bed.split7986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7987 0 1 2 100 hg38.150200.bed.split7987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7988 0 1 2 100 hg38.150200.bed.split7988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7989 0 1 2 100 hg38.150200.bed.split7989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split799 0 1 2 100 hg38.150200.bed.split799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7990 0 1 2 100 hg38.150200.bed.split7990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7991 0 1 2 100 hg38.150200.bed.split7991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7992 0 1 2 100 hg38.150200.bed.split7992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7993 0 1 2 100 hg38.150200.bed.split7993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7994 0 1 2 100 hg38.150200.bed.split7994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7995 0 1 2 100 hg38.150200.bed.split7995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7996 0 1 2 100 hg38.150200.bed.split7996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7997 0 1 2 100 hg38.150200.bed.split7997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7998 0 1 2 100 hg38.150200.bed.split7998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split7999 0 1 2 100 hg38.150200.bed.split7999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8 0 1 2 100 hg38.150200.bed.split8.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split80 0 1 2 100 hg38.150200.bed.split80.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split800 0 1 2 100 hg38.150200.bed.split800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8000 0 1 2 100 hg38.150200.bed.split8000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8001 0 1 2 100 hg38.150200.bed.split8001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8002 0 1 2 100 hg38.150200.bed.split8002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8003 0 1 2 100 hg38.150200.bed.split8003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8004 0 1 2 100 hg38.150200.bed.split8004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8005 0 1 2 100 hg38.150200.bed.split8005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8006 0 1 2 100 hg38.150200.bed.split8006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8007 0 1 2 100 hg38.150200.bed.split8007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8008 0 1 2 100 hg38.150200.bed.split8008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8009 0 1 2 100 hg38.150200.bed.split8009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split801 0 1 2 100 hg38.150200.bed.split801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8010 0 1 2 100 hg38.150200.bed.split8010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8011 0 1 2 100 hg38.150200.bed.split8011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8012 0 1 2 100 hg38.150200.bed.split8012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8013 0 1 2 100 hg38.150200.bed.split8013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8014 0 1 2 100 hg38.150200.bed.split8014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8015 0 1 2 100 hg38.150200.bed.split8015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8016 0 1 2 100 hg38.150200.bed.split8016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8017 0 1 2 100 hg38.150200.bed.split8017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8018 0 1 2 100 hg38.150200.bed.split8018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8019 0 1 2 100 hg38.150200.bed.split8019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split802 0 1 2 100 hg38.150200.bed.split802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8020 0 1 2 100 hg38.150200.bed.split8020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8021 0 1 2 100 hg38.150200.bed.split8021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8022 0 1 2 100 hg38.150200.bed.split8022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8023 0 1 2 100 hg38.150200.bed.split8023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8024 0 1 2 100 hg38.150200.bed.split8024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8025 0 1 2 100 hg38.150200.bed.split8025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8026 0 1 2 100 hg38.150200.bed.split8026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8027 0 1 2 100 hg38.150200.bed.split8027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8028 0 1 2 100 hg38.150200.bed.split8028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8029 0 1 2 100 hg38.150200.bed.split8029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split803 0 1 2 100 hg38.150200.bed.split803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8030 0 1 2 100 hg38.150200.bed.split8030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8031 0 1 2 100 hg38.150200.bed.split8031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8032 0 1 2 100 hg38.150200.bed.split8032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8033 0 1 2 100 hg38.150200.bed.split8033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8034 0 1 2 100 hg38.150200.bed.split8034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8035 0 1 2 100 hg38.150200.bed.split8035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8036 0 1 2 100 hg38.150200.bed.split8036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8037 0 1 2 100 hg38.150200.bed.split8037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8038 0 1 2 100 hg38.150200.bed.split8038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8039 0 1 2 100 hg38.150200.bed.split8039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split804 0 1 2 100 hg38.150200.bed.split804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8040 0 1 2 100 hg38.150200.bed.split8040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8041 0 1 2 100 hg38.150200.bed.split8041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8042 0 1 2 100 hg38.150200.bed.split8042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8043 0 1 2 100 hg38.150200.bed.split8043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8044 0 1 2 100 hg38.150200.bed.split8044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8045 0 1 2 100 hg38.150200.bed.split8045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8046 0 1 2 100 hg38.150200.bed.split8046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8047 0 1 2 100 hg38.150200.bed.split8047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8048 0 1 2 100 hg38.150200.bed.split8048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8049 0 1 2 100 hg38.150200.bed.split8049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split805 0 1 2 100 hg38.150200.bed.split805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8050 0 1 2 100 hg38.150200.bed.split8050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8051 0 1 2 100 hg38.150200.bed.split8051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8052 0 1 2 100 hg38.150200.bed.split8052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8053 0 1 2 100 hg38.150200.bed.split8053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8054 0 1 2 100 hg38.150200.bed.split8054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8055 0 1 2 100 hg38.150200.bed.split8055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8056 0 1 2 100 hg38.150200.bed.split8056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8057 0 1 2 100 hg38.150200.bed.split8057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8058 0 1 2 100 hg38.150200.bed.split8058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8059 0 1 2 100 hg38.150200.bed.split8059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split806 0 1 2 100 hg38.150200.bed.split806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8060 0 1 2 100 hg38.150200.bed.split8060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8061 0 1 2 100 hg38.150200.bed.split8061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8062 0 1 2 100 hg38.150200.bed.split8062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8063 0 1 2 100 hg38.150200.bed.split8063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8064 0 1 2 100 hg38.150200.bed.split8064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8065 0 1 2 100 hg38.150200.bed.split8065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8066 0 1 2 100 hg38.150200.bed.split8066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8067 0 1 2 100 hg38.150200.bed.split8067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8068 0 1 2 100 hg38.150200.bed.split8068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8069 0 1 2 100 hg38.150200.bed.split8069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split807 0 1 2 100 hg38.150200.bed.split807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8070 0 1 2 100 hg38.150200.bed.split8070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8071 0 1 2 100 hg38.150200.bed.split8071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8072 0 1 2 100 hg38.150200.bed.split8072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8073 0 1 2 100 hg38.150200.bed.split8073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8074 0 1 2 100 hg38.150200.bed.split8074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8075 0 1 2 100 hg38.150200.bed.split8075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8076 0 1 2 100 hg38.150200.bed.split8076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8077 0 1 2 100 hg38.150200.bed.split8077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8078 0 1 2 100 hg38.150200.bed.split8078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8079 0 1 2 100 hg38.150200.bed.split8079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split808 0 1 2 100 hg38.150200.bed.split808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8080 0 1 2 100 hg38.150200.bed.split8080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8081 0 1 2 100 hg38.150200.bed.split8081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8082 0 1 2 100 hg38.150200.bed.split8082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8083 0 1 2 100 hg38.150200.bed.split8083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8084 0 1 2 100 hg38.150200.bed.split8084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8085 0 1 2 100 hg38.150200.bed.split8085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8086 0 1 2 100 hg38.150200.bed.split8086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8087 0 1 2 100 hg38.150200.bed.split8087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8088 0 1 2 100 hg38.150200.bed.split8088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8089 0 1 2 100 hg38.150200.bed.split8089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split809 0 1 2 100 hg38.150200.bed.split809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8090 0 1 2 100 hg38.150200.bed.split8090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8091 0 1 2 100 hg38.150200.bed.split8091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8092 0 1 2 100 hg38.150200.bed.split8092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8093 0 1 2 100 hg38.150200.bed.split8093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8094 0 1 2 100 hg38.150200.bed.split8094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8095 0 1 2 100 hg38.150200.bed.split8095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8096 0 1 2 100 hg38.150200.bed.split8096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8097 0 1 2 100 hg38.150200.bed.split8097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8098 0 1 2 100 hg38.150200.bed.split8098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8099 0 1 2 100 hg38.150200.bed.split8099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split81 0 1 2 100 hg38.150200.bed.split81.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split810 0 1 2 100 hg38.150200.bed.split810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8100 0 1 2 100 hg38.150200.bed.split8100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8101 0 1 2 100 hg38.150200.bed.split8101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8102 0 1 2 100 hg38.150200.bed.split8102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8103 0 1 2 100 hg38.150200.bed.split8103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8104 0 1 2 100 hg38.150200.bed.split8104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8105 0 1 2 100 hg38.150200.bed.split8105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8106 0 1 2 100 hg38.150200.bed.split8106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8107 0 1 2 100 hg38.150200.bed.split8107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8108 0 1 2 100 hg38.150200.bed.split8108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8109 0 1 2 100 hg38.150200.bed.split8109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split811 0 1 2 100 hg38.150200.bed.split811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8110 0 1 2 100 hg38.150200.bed.split8110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8111 0 1 2 100 hg38.150200.bed.split8111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8112 0 1 2 100 hg38.150200.bed.split8112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8113 0 1 2 100 hg38.150200.bed.split8113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8114 0 1 2 100 hg38.150200.bed.split8114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8115 0 1 2 100 hg38.150200.bed.split8115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8116 0 1 2 100 hg38.150200.bed.split8116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8117 0 1 2 100 hg38.150200.bed.split8117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8118 0 1 2 100 hg38.150200.bed.split8118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8119 0 1 2 100 hg38.150200.bed.split8119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split812 0 1 2 100 hg38.150200.bed.split812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8120 0 1 2 100 hg38.150200.bed.split8120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8121 0 1 2 100 hg38.150200.bed.split8121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8122 0 1 2 100 hg38.150200.bed.split8122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8123 0 1 2 100 hg38.150200.bed.split8123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8124 0 1 2 100 hg38.150200.bed.split8124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8125 0 1 2 100 hg38.150200.bed.split8125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8126 0 1 2 100 hg38.150200.bed.split8126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8127 0 1 2 100 hg38.150200.bed.split8127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8128 0 1 2 100 hg38.150200.bed.split8128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8129 0 1 2 100 hg38.150200.bed.split8129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split813 0 1 2 100 hg38.150200.bed.split813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8130 0 1 2 100 hg38.150200.bed.split8130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8131 0 1 2 100 hg38.150200.bed.split8131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8132 0 1 2 100 hg38.150200.bed.split8132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8133 0 1 2 100 hg38.150200.bed.split8133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8134 0 1 2 100 hg38.150200.bed.split8134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8135 0 1 2 100 hg38.150200.bed.split8135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8136 0 1 2 100 hg38.150200.bed.split8136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8137 0 1 2 100 hg38.150200.bed.split8137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8138 0 1 2 100 hg38.150200.bed.split8138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8139 0 1 2 100 hg38.150200.bed.split8139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split814 0 1 2 100 hg38.150200.bed.split814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8140 0 1 2 100 hg38.150200.bed.split8140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8141 0 1 2 100 hg38.150200.bed.split8141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8142 0 1 2 100 hg38.150200.bed.split8142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8143 0 1 2 100 hg38.150200.bed.split8143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8144 0 1 2 100 hg38.150200.bed.split8144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8145 0 1 2 100 hg38.150200.bed.split8145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8146 0 1 2 100 hg38.150200.bed.split8146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8147 0 1 2 100 hg38.150200.bed.split8147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8148 0 1 2 100 hg38.150200.bed.split8148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8149 0 1 2 100 hg38.150200.bed.split8149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split815 0 1 2 100 hg38.150200.bed.split815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8150 0 1 2 100 hg38.150200.bed.split8150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8151 0 1 2 100 hg38.150200.bed.split8151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8152 0 1 2 100 hg38.150200.bed.split8152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8153 0 1 2 100 hg38.150200.bed.split8153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8154 0 1 2 100 hg38.150200.bed.split8154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8155 0 1 2 100 hg38.150200.bed.split8155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8156 0 1 2 100 hg38.150200.bed.split8156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8157 0 1 2 100 hg38.150200.bed.split8157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8158 0 1 2 100 hg38.150200.bed.split8158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8159 0 1 2 100 hg38.150200.bed.split8159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split816 0 1 2 100 hg38.150200.bed.split816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8160 0 1 2 100 hg38.150200.bed.split8160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8161 0 1 2 100 hg38.150200.bed.split8161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8162 0 1 2 100 hg38.150200.bed.split8162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8163 0 1 2 100 hg38.150200.bed.split8163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8164 0 1 2 100 hg38.150200.bed.split8164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8165 0 1 2 100 hg38.150200.bed.split8165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8166 0 1 2 100 hg38.150200.bed.split8166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8167 0 1 2 100 hg38.150200.bed.split8167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8168 0 1 2 100 hg38.150200.bed.split8168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8169 0 1 2 100 hg38.150200.bed.split8169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split817 0 1 2 100 hg38.150200.bed.split817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8170 0 1 2 100 hg38.150200.bed.split8170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8171 0 1 2 100 hg38.150200.bed.split8171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8172 0 1 2 100 hg38.150200.bed.split8172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8173 0 1 2 100 hg38.150200.bed.split8173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8174 0 1 2 100 hg38.150200.bed.split8174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8175 0 1 2 100 hg38.150200.bed.split8175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8176 0 1 2 100 hg38.150200.bed.split8176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8177 0 1 2 100 hg38.150200.bed.split8177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8178 0 1 2 100 hg38.150200.bed.split8178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8179 0 1 2 100 hg38.150200.bed.split8179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split818 0 1 2 100 hg38.150200.bed.split818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8180 0 1 2 100 hg38.150200.bed.split8180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8181 0 1 2 100 hg38.150200.bed.split8181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8182 0 1 2 100 hg38.150200.bed.split8182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8183 0 1 2 100 hg38.150200.bed.split8183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8184 0 1 2 100 hg38.150200.bed.split8184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8185 0 1 2 100 hg38.150200.bed.split8185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8186 0 1 2 100 hg38.150200.bed.split8186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8187 0 1 2 100 hg38.150200.bed.split8187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8188 0 1 2 100 hg38.150200.bed.split8188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8189 0 1 2 100 hg38.150200.bed.split8189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split819 0 1 2 100 hg38.150200.bed.split819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8190 0 1 2 100 hg38.150200.bed.split8190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8191 0 1 2 100 hg38.150200.bed.split8191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8192 0 1 2 100 hg38.150200.bed.split8192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8193 0 1 2 100 hg38.150200.bed.split8193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8194 0 1 2 100 hg38.150200.bed.split8194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8195 0 1 2 100 hg38.150200.bed.split8195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8196 0 1 2 100 hg38.150200.bed.split8196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8197 0 1 2 100 hg38.150200.bed.split8197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8198 0 1 2 100 hg38.150200.bed.split8198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8199 0 1 2 100 hg38.150200.bed.split8199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split82 0 1 2 100 hg38.150200.bed.split82.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split820 0 1 2 100 hg38.150200.bed.split820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8200 0 1 2 100 hg38.150200.bed.split8200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8201 0 1 2 100 hg38.150200.bed.split8201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8202 0 1 2 100 hg38.150200.bed.split8202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8203 0 1 2 100 hg38.150200.bed.split8203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8204 0 1 2 100 hg38.150200.bed.split8204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8205 0 1 2 100 hg38.150200.bed.split8205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8206 0 1 2 100 hg38.150200.bed.split8206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8207 0 1 2 100 hg38.150200.bed.split8207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8208 0 1 2 100 hg38.150200.bed.split8208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8209 0 1 2 100 hg38.150200.bed.split8209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split821 0 1 2 100 hg38.150200.bed.split821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8210 0 1 2 100 hg38.150200.bed.split8210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8211 0 1 2 100 hg38.150200.bed.split8211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8212 0 1 2 100 hg38.150200.bed.split8212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8213 0 1 2 100 hg38.150200.bed.split8213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8214 0 1 2 100 hg38.150200.bed.split8214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8215 0 1 2 100 hg38.150200.bed.split8215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8216 0 1 2 100 hg38.150200.bed.split8216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8217 0 1 2 100 hg38.150200.bed.split8217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8218 0 1 2 100 hg38.150200.bed.split8218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8219 0 1 2 100 hg38.150200.bed.split8219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split822 0 1 2 100 hg38.150200.bed.split822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8220 0 1 2 100 hg38.150200.bed.split8220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8221 0 1 2 100 hg38.150200.bed.split8221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8222 0 1 2 100 hg38.150200.bed.split8222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8223 0 1 2 100 hg38.150200.bed.split8223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8224 0 1 2 100 hg38.150200.bed.split8224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8225 0 1 2 100 hg38.150200.bed.split8225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8226 0 1 2 100 hg38.150200.bed.split8226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8227 0 1 2 100 hg38.150200.bed.split8227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8228 0 1 2 100 hg38.150200.bed.split8228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8229 0 1 2 100 hg38.150200.bed.split8229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split823 0 1 2 100 hg38.150200.bed.split823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8230 0 1 2 100 hg38.150200.bed.split8230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8231 0 1 2 100 hg38.150200.bed.split8231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8232 0 1 2 100 hg38.150200.bed.split8232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8233 0 1 2 100 hg38.150200.bed.split8233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8234 0 1 2 100 hg38.150200.bed.split8234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8235 0 1 2 100 hg38.150200.bed.split8235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8236 0 1 2 100 hg38.150200.bed.split8236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8237 0 1 2 100 hg38.150200.bed.split8237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8238 0 1 2 100 hg38.150200.bed.split8238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8239 0 1 2 100 hg38.150200.bed.split8239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split824 0 1 2 100 hg38.150200.bed.split824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8240 0 1 2 100 hg38.150200.bed.split8240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8241 0 1 2 100 hg38.150200.bed.split8241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8242 0 1 2 100 hg38.150200.bed.split8242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8243 0 1 2 100 hg38.150200.bed.split8243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8244 0 1 2 100 hg38.150200.bed.split8244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8245 0 1 2 100 hg38.150200.bed.split8245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8246 0 1 2 100 hg38.150200.bed.split8246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8247 0 1 2 100 hg38.150200.bed.split8247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8248 0 1 2 100 hg38.150200.bed.split8248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8249 0 1 2 100 hg38.150200.bed.split8249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split825 0 1 2 100 hg38.150200.bed.split825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8250 0 1 2 100 hg38.150200.bed.split8250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8251 0 1 2 100 hg38.150200.bed.split8251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8252 0 1 2 100 hg38.150200.bed.split8252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8253 0 1 2 100 hg38.150200.bed.split8253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8254 0 1 2 100 hg38.150200.bed.split8254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8255 0 1 2 100 hg38.150200.bed.split8255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8256 0 1 2 100 hg38.150200.bed.split8256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8257 0 1 2 100 hg38.150200.bed.split8257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8258 0 1 2 100 hg38.150200.bed.split8258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8259 0 1 2 100 hg38.150200.bed.split8259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split826 0 1 2 100 hg38.150200.bed.split826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8260 0 1 2 100 hg38.150200.bed.split8260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8261 0 1 2 100 hg38.150200.bed.split8261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8262 0 1 2 100 hg38.150200.bed.split8262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8263 0 1 2 100 hg38.150200.bed.split8263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8264 0 1 2 100 hg38.150200.bed.split8264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8265 0 1 2 100 hg38.150200.bed.split8265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8266 0 1 2 100 hg38.150200.bed.split8266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8267 0 1 2 100 hg38.150200.bed.split8267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8268 0 1 2 100 hg38.150200.bed.split8268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8269 0 1 2 100 hg38.150200.bed.split8269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split827 0 1 2 100 hg38.150200.bed.split827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8270 0 1 2 100 hg38.150200.bed.split8270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8271 0 1 2 100 hg38.150200.bed.split8271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8272 0 1 2 100 hg38.150200.bed.split8272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8273 0 1 2 100 hg38.150200.bed.split8273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8274 0 1 2 100 hg38.150200.bed.split8274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8275 0 1 2 100 hg38.150200.bed.split8275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8276 0 1 2 100 hg38.150200.bed.split8276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8277 0 1 2 100 hg38.150200.bed.split8277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8278 0 1 2 100 hg38.150200.bed.split8278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8279 0 1 2 100 hg38.150200.bed.split8279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split828 0 1 2 100 hg38.150200.bed.split828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8280 0 1 2 100 hg38.150200.bed.split8280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8281 0 1 2 100 hg38.150200.bed.split8281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8282 0 1 2 100 hg38.150200.bed.split8282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8283 0 1 2 100 hg38.150200.bed.split8283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8284 0 1 2 100 hg38.150200.bed.split8284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8285 0 1 2 100 hg38.150200.bed.split8285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8286 0 1 2 100 hg38.150200.bed.split8286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8287 0 1 2 100 hg38.150200.bed.split8287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8288 0 1 2 100 hg38.150200.bed.split8288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8289 0 1 2 100 hg38.150200.bed.split8289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split829 0 1 2 100 hg38.150200.bed.split829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8290 0 1 2 100 hg38.150200.bed.split8290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8291 0 1 2 100 hg38.150200.bed.split8291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8292 0 1 2 100 hg38.150200.bed.split8292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8293 0 1 2 100 hg38.150200.bed.split8293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8294 0 1 2 100 hg38.150200.bed.split8294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8295 0 1 2 100 hg38.150200.bed.split8295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8296 0 1 2 100 hg38.150200.bed.split8296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8297 0 1 2 100 hg38.150200.bed.split8297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8298 0 1 2 100 hg38.150200.bed.split8298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8299 0 1 2 100 hg38.150200.bed.split8299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split83 0 1 2 100 hg38.150200.bed.split83.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split830 0 1 2 100 hg38.150200.bed.split830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8300 0 1 2 100 hg38.150200.bed.split8300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8301 0 1 2 100 hg38.150200.bed.split8301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8302 0 1 2 100 hg38.150200.bed.split8302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8303 0 1 2 100 hg38.150200.bed.split8303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8304 0 1 2 100 hg38.150200.bed.split8304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8305 0 1 2 100 hg38.150200.bed.split8305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8306 0 1 2 100 hg38.150200.bed.split8306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8307 0 1 2 100 hg38.150200.bed.split8307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8308 0 1 2 100 hg38.150200.bed.split8308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8309 0 1 2 100 hg38.150200.bed.split8309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split831 0 1 2 100 hg38.150200.bed.split831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8310 0 1 2 100 hg38.150200.bed.split8310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8311 0 1 2 100 hg38.150200.bed.split8311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8312 0 1 2 100 hg38.150200.bed.split8312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8313 0 1 2 100 hg38.150200.bed.split8313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8314 0 1 2 100 hg38.150200.bed.split8314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8315 0 1 2 100 hg38.150200.bed.split8315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8316 0 1 2 100 hg38.150200.bed.split8316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8317 0 1 2 100 hg38.150200.bed.split8317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8318 0 1 2 100 hg38.150200.bed.split8318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8319 0 1 2 100 hg38.150200.bed.split8319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split832 0 1 2 100 hg38.150200.bed.split832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8320 0 1 2 100 hg38.150200.bed.split8320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8321 0 1 2 100 hg38.150200.bed.split8321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8322 0 1 2 100 hg38.150200.bed.split8322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8323 0 1 2 100 hg38.150200.bed.split8323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8324 0 1 2 100 hg38.150200.bed.split8324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8325 0 1 2 100 hg38.150200.bed.split8325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8326 0 1 2 100 hg38.150200.bed.split8326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8327 0 1 2 100 hg38.150200.bed.split8327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8328 0 1 2 100 hg38.150200.bed.split8328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8329 0 1 2 100 hg38.150200.bed.split8329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split833 0 1 2 100 hg38.150200.bed.split833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8330 0 1 2 100 hg38.150200.bed.split8330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8331 0 1 2 100 hg38.150200.bed.split8331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8332 0 1 2 100 hg38.150200.bed.split8332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8333 0 1 2 100 hg38.150200.bed.split8333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8334 0 1 2 100 hg38.150200.bed.split8334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8335 0 1 2 100 hg38.150200.bed.split8335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8336 0 1 2 100 hg38.150200.bed.split8336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8337 0 1 2 100 hg38.150200.bed.split8337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8338 0 1 2 100 hg38.150200.bed.split8338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8339 0 1 2 100 hg38.150200.bed.split8339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split834 0 1 2 100 hg38.150200.bed.split834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8340 0 1 2 100 hg38.150200.bed.split8340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8341 0 1 2 100 hg38.150200.bed.split8341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8342 0 1 2 100 hg38.150200.bed.split8342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8343 0 1 2 100 hg38.150200.bed.split8343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8344 0 1 2 100 hg38.150200.bed.split8344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8345 0 1 2 100 hg38.150200.bed.split8345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8346 0 1 2 100 hg38.150200.bed.split8346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8347 0 1 2 100 hg38.150200.bed.split8347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8348 0 1 2 100 hg38.150200.bed.split8348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8349 0 1 2 100 hg38.150200.bed.split8349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split835 0 1 2 100 hg38.150200.bed.split835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8350 0 1 2 100 hg38.150200.bed.split8350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8351 0 1 2 100 hg38.150200.bed.split8351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8352 0 1 2 100 hg38.150200.bed.split8352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8353 0 1 2 100 hg38.150200.bed.split8353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8354 0 1 2 100 hg38.150200.bed.split8354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8355 0 1 2 100 hg38.150200.bed.split8355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8356 0 1 2 100 hg38.150200.bed.split8356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8357 0 1 2 100 hg38.150200.bed.split8357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8358 0 1 2 100 hg38.150200.bed.split8358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8359 0 1 2 100 hg38.150200.bed.split8359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split836 0 1 2 100 hg38.150200.bed.split836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8360 0 1 2 100 hg38.150200.bed.split8360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8361 0 1 2 100 hg38.150200.bed.split8361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8362 0 1 2 100 hg38.150200.bed.split8362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8363 0 1 2 100 hg38.150200.bed.split8363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8364 0 1 2 100 hg38.150200.bed.split8364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8365 0 1 2 100 hg38.150200.bed.split8365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8366 0 1 2 100 hg38.150200.bed.split8366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8367 0 1 2 100 hg38.150200.bed.split8367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8368 0 1 2 100 hg38.150200.bed.split8368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8369 0 1 2 100 hg38.150200.bed.split8369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split837 0 1 2 100 hg38.150200.bed.split837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8370 0 1 2 100 hg38.150200.bed.split8370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8371 0 1 2 100 hg38.150200.bed.split8371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8372 0 1 2 100 hg38.150200.bed.split8372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8373 0 1 2 100 hg38.150200.bed.split8373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8374 0 1 2 100 hg38.150200.bed.split8374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8375 0 1 2 100 hg38.150200.bed.split8375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8376 0 1 2 100 hg38.150200.bed.split8376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8377 0 1 2 100 hg38.150200.bed.split8377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8378 0 1 2 100 hg38.150200.bed.split8378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8379 0 1 2 100 hg38.150200.bed.split8379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split838 0 1 2 100 hg38.150200.bed.split838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8380 0 1 2 100 hg38.150200.bed.split8380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8381 0 1 2 100 hg38.150200.bed.split8381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8382 0 1 2 100 hg38.150200.bed.split8382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8383 0 1 2 100 hg38.150200.bed.split8383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8384 0 1 2 100 hg38.150200.bed.split8384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8385 0 1 2 100 hg38.150200.bed.split8385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8386 0 1 2 100 hg38.150200.bed.split8386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8387 0 1 2 100 hg38.150200.bed.split8387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8388 0 1 2 100 hg38.150200.bed.split8388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8389 0 1 2 100 hg38.150200.bed.split8389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split839 0 1 2 100 hg38.150200.bed.split839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8390 0 1 2 100 hg38.150200.bed.split8390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8391 0 1 2 100 hg38.150200.bed.split8391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8392 0 1 2 100 hg38.150200.bed.split8392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8393 0 1 2 100 hg38.150200.bed.split8393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8394 0 1 2 100 hg38.150200.bed.split8394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8395 0 1 2 100 hg38.150200.bed.split8395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8396 0 1 2 100 hg38.150200.bed.split8396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8397 0 1 2 100 hg38.150200.bed.split8397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8398 0 1 2 100 hg38.150200.bed.split8398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8399 0 1 2 100 hg38.150200.bed.split8399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split84 0 1 2 100 hg38.150200.bed.split84.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split840 0 1 2 100 hg38.150200.bed.split840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8400 0 1 2 100 hg38.150200.bed.split8400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8401 0 1 2 100 hg38.150200.bed.split8401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8402 0 1 2 100 hg38.150200.bed.split8402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8403 0 1 2 100 hg38.150200.bed.split8403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8404 0 1 2 100 hg38.150200.bed.split8404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8405 0 1 2 100 hg38.150200.bed.split8405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8406 0 1 2 100 hg38.150200.bed.split8406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8407 0 1 2 100 hg38.150200.bed.split8407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8408 0 1 2 100 hg38.150200.bed.split8408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8409 0 1 2 100 hg38.150200.bed.split8409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split841 0 1 2 100 hg38.150200.bed.split841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8410 0 1 2 100 hg38.150200.bed.split8410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8411 0 1 2 100 hg38.150200.bed.split8411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8412 0 1 2 100 hg38.150200.bed.split8412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8413 0 1 2 100 hg38.150200.bed.split8413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8414 0 1 2 100 hg38.150200.bed.split8414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8415 0 1 2 100 hg38.150200.bed.split8415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8416 0 1 2 100 hg38.150200.bed.split8416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8417 0 1 2 100 hg38.150200.bed.split8417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8418 0 1 2 100 hg38.150200.bed.split8418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8419 0 1 2 100 hg38.150200.bed.split8419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split842 0 1 2 100 hg38.150200.bed.split842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8420 0 1 2 100 hg38.150200.bed.split8420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8421 0 1 2 100 hg38.150200.bed.split8421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8422 0 1 2 100 hg38.150200.bed.split8422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8423 0 1 2 100 hg38.150200.bed.split8423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8424 0 1 2 100 hg38.150200.bed.split8424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8425 0 1 2 100 hg38.150200.bed.split8425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8426 0 1 2 100 hg38.150200.bed.split8426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8427 0 1 2 100 hg38.150200.bed.split8427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8428 0 1 2 100 hg38.150200.bed.split8428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8429 0 1 2 100 hg38.150200.bed.split8429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split843 0 1 2 100 hg38.150200.bed.split843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8430 0 1 2 100 hg38.150200.bed.split8430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8431 0 1 2 100 hg38.150200.bed.split8431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8432 0 1 2 100 hg38.150200.bed.split8432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8433 0 1 2 100 hg38.150200.bed.split8433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8434 0 1 2 100 hg38.150200.bed.split8434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8435 0 1 2 100 hg38.150200.bed.split8435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8436 0 1 2 100 hg38.150200.bed.split8436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8437 0 1 2 100 hg38.150200.bed.split8437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8438 0 1 2 100 hg38.150200.bed.split8438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8439 0 1 2 100 hg38.150200.bed.split8439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split844 0 1 2 100 hg38.150200.bed.split844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8440 0 1 2 100 hg38.150200.bed.split8440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8441 0 1 2 100 hg38.150200.bed.split8441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8442 0 1 2 100 hg38.150200.bed.split8442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8443 0 1 2 100 hg38.150200.bed.split8443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8444 0 1 2 100 hg38.150200.bed.split8444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8445 0 1 2 100 hg38.150200.bed.split8445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8446 0 1 2 100 hg38.150200.bed.split8446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8447 0 1 2 100 hg38.150200.bed.split8447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8448 0 1 2 100 hg38.150200.bed.split8448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8449 0 1 2 100 hg38.150200.bed.split8449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split845 0 1 2 100 hg38.150200.bed.split845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8450 0 1 2 100 hg38.150200.bed.split8450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8451 0 1 2 100 hg38.150200.bed.split8451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8452 0 1 2 100 hg38.150200.bed.split8452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8453 0 1 2 100 hg38.150200.bed.split8453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8454 0 1 2 100 hg38.150200.bed.split8454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8455 0 1 2 100 hg38.150200.bed.split8455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8456 0 1 2 100 hg38.150200.bed.split8456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8457 0 1 2 100 hg38.150200.bed.split8457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8458 0 1 2 100 hg38.150200.bed.split8458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8459 0 1 2 100 hg38.150200.bed.split8459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split846 0 1 2 100 hg38.150200.bed.split846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8460 0 1 2 100 hg38.150200.bed.split8460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8461 0 1 2 100 hg38.150200.bed.split8461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8462 0 1 2 100 hg38.150200.bed.split8462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8463 0 1 2 100 hg38.150200.bed.split8463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8464 0 1 2 100 hg38.150200.bed.split8464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8465 0 1 2 100 hg38.150200.bed.split8465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8466 0 1 2 100 hg38.150200.bed.split8466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8467 0 1 2 100 hg38.150200.bed.split8467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8468 0 1 2 100 hg38.150200.bed.split8468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8469 0 1 2 100 hg38.150200.bed.split8469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split847 0 1 2 100 hg38.150200.bed.split847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8470 0 1 2 100 hg38.150200.bed.split8470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8471 0 1 2 100 hg38.150200.bed.split8471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8472 0 1 2 100 hg38.150200.bed.split8472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8473 0 1 2 100 hg38.150200.bed.split8473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8474 0 1 2 100 hg38.150200.bed.split8474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8475 0 1 2 100 hg38.150200.bed.split8475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8476 0 1 2 100 hg38.150200.bed.split8476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8477 0 1 2 100 hg38.150200.bed.split8477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8478 0 1 2 100 hg38.150200.bed.split8478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8479 0 1 2 100 hg38.150200.bed.split8479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split848 0 1 2 100 hg38.150200.bed.split848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8480 0 1 2 100 hg38.150200.bed.split8480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8481 0 1 2 100 hg38.150200.bed.split8481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8482 0 1 2 100 hg38.150200.bed.split8482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8483 0 1 2 100 hg38.150200.bed.split8483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8484 0 1 2 100 hg38.150200.bed.split8484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8485 0 1 2 100 hg38.150200.bed.split8485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8486 0 1 2 100 hg38.150200.bed.split8486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8487 0 1 2 100 hg38.150200.bed.split8487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8488 0 1 2 100 hg38.150200.bed.split8488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8489 0 1 2 100 hg38.150200.bed.split8489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split849 0 1 2 100 hg38.150200.bed.split849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8490 0 1 2 100 hg38.150200.bed.split8490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8491 0 1 2 100 hg38.150200.bed.split8491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8492 0 1 2 100 hg38.150200.bed.split8492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8493 0 1 2 100 hg38.150200.bed.split8493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8494 0 1 2 100 hg38.150200.bed.split8494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8495 0 1 2 100 hg38.150200.bed.split8495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8496 0 1 2 100 hg38.150200.bed.split8496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8497 0 1 2 100 hg38.150200.bed.split8497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8498 0 1 2 100 hg38.150200.bed.split8498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8499 0 1 2 100 hg38.150200.bed.split8499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split85 0 1 2 100 hg38.150200.bed.split85.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split850 0 1 2 100 hg38.150200.bed.split850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8500 0 1 2 100 hg38.150200.bed.split8500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8501 0 1 2 100 hg38.150200.bed.split8501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8502 0 1 2 100 hg38.150200.bed.split8502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8503 0 1 2 100 hg38.150200.bed.split8503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8504 0 1 2 100 hg38.150200.bed.split8504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8505 0 1 2 100 hg38.150200.bed.split8505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8506 0 1 2 100 hg38.150200.bed.split8506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8507 0 1 2 100 hg38.150200.bed.split8507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8508 0 1 2 100 hg38.150200.bed.split8508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8509 0 1 2 100 hg38.150200.bed.split8509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split851 0 1 2 100 hg38.150200.bed.split851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8510 0 1 2 100 hg38.150200.bed.split8510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8511 0 1 2 100 hg38.150200.bed.split8511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8512 0 1 2 100 hg38.150200.bed.split8512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8513 0 1 2 100 hg38.150200.bed.split8513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8514 0 1 2 100 hg38.150200.bed.split8514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8515 0 1 2 100 hg38.150200.bed.split8515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8516 0 1 2 100 hg38.150200.bed.split8516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8517 0 1 2 100 hg38.150200.bed.split8517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8518 0 1 2 100 hg38.150200.bed.split8518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8519 0 1 2 100 hg38.150200.bed.split8519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split852 0 1 2 100 hg38.150200.bed.split852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8520 0 1 2 100 hg38.150200.bed.split8520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8521 0 1 2 100 hg38.150200.bed.split8521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8522 0 1 2 100 hg38.150200.bed.split8522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8523 0 1 2 100 hg38.150200.bed.split8523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8524 0 1 2 100 hg38.150200.bed.split8524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8525 0 1 2 100 hg38.150200.bed.split8525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8526 0 1 2 100 hg38.150200.bed.split8526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8527 0 1 2 100 hg38.150200.bed.split8527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8528 0 1 2 100 hg38.150200.bed.split8528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8529 0 1 2 100 hg38.150200.bed.split8529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split853 0 1 2 100 hg38.150200.bed.split853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8530 0 1 2 100 hg38.150200.bed.split8530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8531 0 1 2 100 hg38.150200.bed.split8531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8532 0 1 2 100 hg38.150200.bed.split8532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8533 0 1 2 100 hg38.150200.bed.split8533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8534 0 1 2 100 hg38.150200.bed.split8534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8535 0 1 2 100 hg38.150200.bed.split8535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8536 0 1 2 100 hg38.150200.bed.split8536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8537 0 1 2 100 hg38.150200.bed.split8537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8538 0 1 2 100 hg38.150200.bed.split8538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8539 0 1 2 100 hg38.150200.bed.split8539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split854 0 1 2 100 hg38.150200.bed.split854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8540 0 1 2 100 hg38.150200.bed.split8540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8541 0 1 2 100 hg38.150200.bed.split8541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8542 0 1 2 100 hg38.150200.bed.split8542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8543 0 1 2 100 hg38.150200.bed.split8543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8544 0 1 2 100 hg38.150200.bed.split8544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8545 0 1 2 100 hg38.150200.bed.split8545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8546 0 1 2 100 hg38.150200.bed.split8546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8547 0 1 2 100 hg38.150200.bed.split8547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8548 0 1 2 100 hg38.150200.bed.split8548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8549 0 1 2 100 hg38.150200.bed.split8549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split855 0 1 2 100 hg38.150200.bed.split855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8550 0 1 2 100 hg38.150200.bed.split8550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8551 0 1 2 100 hg38.150200.bed.split8551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8552 0 1 2 100 hg38.150200.bed.split8552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8553 0 1 2 100 hg38.150200.bed.split8553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8554 0 1 2 100 hg38.150200.bed.split8554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8555 0 1 2 100 hg38.150200.bed.split8555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8556 0 1 2 100 hg38.150200.bed.split8556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8557 0 1 2 100 hg38.150200.bed.split8557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8558 0 1 2 100 hg38.150200.bed.split8558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8559 0 1 2 100 hg38.150200.bed.split8559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split856 0 1 2 100 hg38.150200.bed.split856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8560 0 1 2 100 hg38.150200.bed.split8560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8561 0 1 2 100 hg38.150200.bed.split8561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8562 0 1 2 100 hg38.150200.bed.split8562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8563 0 1 2 100 hg38.150200.bed.split8563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8564 0 1 2 100 hg38.150200.bed.split8564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8565 0 1 2 100 hg38.150200.bed.split8565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8566 0 1 2 100 hg38.150200.bed.split8566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8567 0 1 2 100 hg38.150200.bed.split8567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8568 0 1 2 100 hg38.150200.bed.split8568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8569 0 1 2 100 hg38.150200.bed.split8569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split857 0 1 2 100 hg38.150200.bed.split857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8570 0 1 2 100 hg38.150200.bed.split8570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8571 0 1 2 100 hg38.150200.bed.split8571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8572 0 1 2 100 hg38.150200.bed.split8572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8573 0 1 2 100 hg38.150200.bed.split8573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8574 0 1 2 100 hg38.150200.bed.split8574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8575 0 1 2 100 hg38.150200.bed.split8575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8576 0 1 2 100 hg38.150200.bed.split8576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8577 0 1 2 100 hg38.150200.bed.split8577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8578 0 1 2 100 hg38.150200.bed.split8578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8579 0 1 2 100 hg38.150200.bed.split8579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split858 0 1 2 100 hg38.150200.bed.split858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8580 0 1 2 100 hg38.150200.bed.split8580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8581 0 1 2 100 hg38.150200.bed.split8581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8582 0 1 2 100 hg38.150200.bed.split8582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8583 0 1 2 100 hg38.150200.bed.split8583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8584 0 1 2 100 hg38.150200.bed.split8584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8585 0 1 2 100 hg38.150200.bed.split8585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8586 0 1 2 100 hg38.150200.bed.split8586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8587 0 1 2 100 hg38.150200.bed.split8587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8588 0 1 2 100 hg38.150200.bed.split8588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8589 0 1 2 100 hg38.150200.bed.split8589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split859 0 1 2 100 hg38.150200.bed.split859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8590 0 1 2 100 hg38.150200.bed.split8590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8591 0 1 2 100 hg38.150200.bed.split8591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8592 0 1 2 100 hg38.150200.bed.split8592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8593 0 1 2 100 hg38.150200.bed.split8593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8594 0 1 2 100 hg38.150200.bed.split8594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8595 0 1 2 100 hg38.150200.bed.split8595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8596 0 1 2 100 hg38.150200.bed.split8596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8597 0 1 2 100 hg38.150200.bed.split8597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8598 0 1 2 100 hg38.150200.bed.split8598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8599 0 1 2 100 hg38.150200.bed.split8599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split86 0 1 2 100 hg38.150200.bed.split86.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split860 0 1 2 100 hg38.150200.bed.split860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8600 0 1 2 100 hg38.150200.bed.split8600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8601 0 1 2 100 hg38.150200.bed.split8601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8602 0 1 2 100 hg38.150200.bed.split8602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8603 0 1 2 100 hg38.150200.bed.split8603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8604 0 1 2 100 hg38.150200.bed.split8604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8605 0 1 2 100 hg38.150200.bed.split8605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8606 0 1 2 100 hg38.150200.bed.split8606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8607 0 1 2 100 hg38.150200.bed.split8607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8608 0 1 2 100 hg38.150200.bed.split8608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8609 0 1 2 100 hg38.150200.bed.split8609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split861 0 1 2 100 hg38.150200.bed.split861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8610 0 1 2 100 hg38.150200.bed.split8610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8611 0 1 2 100 hg38.150200.bed.split8611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8612 0 1 2 100 hg38.150200.bed.split8612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8613 0 1 2 100 hg38.150200.bed.split8613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8614 0 1 2 100 hg38.150200.bed.split8614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8615 0 1 2 100 hg38.150200.bed.split8615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8616 0 1 2 100 hg38.150200.bed.split8616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8617 0 1 2 100 hg38.150200.bed.split8617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8618 0 1 2 100 hg38.150200.bed.split8618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8619 0 1 2 100 hg38.150200.bed.split8619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split862 0 1 2 100 hg38.150200.bed.split862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8620 0 1 2 100 hg38.150200.bed.split8620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8621 0 1 2 100 hg38.150200.bed.split8621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8622 0 1 2 100 hg38.150200.bed.split8622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8623 0 1 2 100 hg38.150200.bed.split8623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8624 0 1 2 100 hg38.150200.bed.split8624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8625 0 1 2 100 hg38.150200.bed.split8625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8626 0 1 2 100 hg38.150200.bed.split8626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8627 0 1 2 100 hg38.150200.bed.split8627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8628 0 1 2 100 hg38.150200.bed.split8628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8629 0 1 2 100 hg38.150200.bed.split8629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split863 0 1 2 100 hg38.150200.bed.split863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8630 0 1 2 100 hg38.150200.bed.split8630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8631 0 1 2 100 hg38.150200.bed.split8631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8632 0 1 2 100 hg38.150200.bed.split8632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8633 0 1 2 100 hg38.150200.bed.split8633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8634 0 1 2 100 hg38.150200.bed.split8634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8635 0 1 2 100 hg38.150200.bed.split8635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8636 0 1 2 100 hg38.150200.bed.split8636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8637 0 1 2 100 hg38.150200.bed.split8637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8638 0 1 2 100 hg38.150200.bed.split8638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8639 0 1 2 100 hg38.150200.bed.split8639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split864 0 1 2 100 hg38.150200.bed.split864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8640 0 1 2 100 hg38.150200.bed.split8640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8641 0 1 2 100 hg38.150200.bed.split8641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8642 0 1 2 100 hg38.150200.bed.split8642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8643 0 1 2 100 hg38.150200.bed.split8643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8644 0 1 2 100 hg38.150200.bed.split8644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8645 0 1 2 100 hg38.150200.bed.split8645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8646 0 1 2 100 hg38.150200.bed.split8646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8647 0 1 2 100 hg38.150200.bed.split8647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8648 0 1 2 100 hg38.150200.bed.split8648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8649 0 1 2 100 hg38.150200.bed.split8649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split865 0 1 2 100 hg38.150200.bed.split865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8650 0 1 2 100 hg38.150200.bed.split8650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8651 0 1 2 100 hg38.150200.bed.split8651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8652 0 1 2 100 hg38.150200.bed.split8652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8653 0 1 2 100 hg38.150200.bed.split8653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8654 0 1 2 100 hg38.150200.bed.split8654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8655 0 1 2 100 hg38.150200.bed.split8655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8656 0 1 2 100 hg38.150200.bed.split8656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8657 0 1 2 100 hg38.150200.bed.split8657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8658 0 1 2 100 hg38.150200.bed.split8658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8659 0 1 2 100 hg38.150200.bed.split8659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split866 0 1 2 100 hg38.150200.bed.split866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8660 0 1 2 100 hg38.150200.bed.split8660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8661 0 1 2 100 hg38.150200.bed.split8661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8662 0 1 2 100 hg38.150200.bed.split8662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8663 0 1 2 100 hg38.150200.bed.split8663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8664 0 1 2 100 hg38.150200.bed.split8664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8665 0 1 2 100 hg38.150200.bed.split8665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8666 0 1 2 100 hg38.150200.bed.split8666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8667 0 1 2 100 hg38.150200.bed.split8667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8668 0 1 2 100 hg38.150200.bed.split8668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8669 0 1 2 100 hg38.150200.bed.split8669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split867 0 1 2 100 hg38.150200.bed.split867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8670 0 1 2 100 hg38.150200.bed.split8670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8671 0 1 2 100 hg38.150200.bed.split8671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8672 0 1 2 100 hg38.150200.bed.split8672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8673 0 1 2 100 hg38.150200.bed.split8673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8674 0 1 2 100 hg38.150200.bed.split8674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8675 0 1 2 100 hg38.150200.bed.split8675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8676 0 1 2 100 hg38.150200.bed.split8676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8677 0 1 2 100 hg38.150200.bed.split8677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8678 0 1 2 100 hg38.150200.bed.split8678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8679 0 1 2 100 hg38.150200.bed.split8679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split868 0 1 2 100 hg38.150200.bed.split868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8680 0 1 2 100 hg38.150200.bed.split8680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8681 0 1 2 100 hg38.150200.bed.split8681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8682 0 1 2 100 hg38.150200.bed.split8682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8683 0 1 2 100 hg38.150200.bed.split8683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8684 0 1 2 100 hg38.150200.bed.split8684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8685 0 1 2 100 hg38.150200.bed.split8685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8686 0 1 2 100 hg38.150200.bed.split8686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8687 0 1 2 100 hg38.150200.bed.split8687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8688 0 1 2 100 hg38.150200.bed.split8688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8689 0 1 2 100 hg38.150200.bed.split8689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split869 0 1 2 100 hg38.150200.bed.split869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8690 0 1 2 100 hg38.150200.bed.split8690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8691 0 1 2 100 hg38.150200.bed.split8691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8692 0 1 2 100 hg38.150200.bed.split8692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8693 0 1 2 100 hg38.150200.bed.split8693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8694 0 1 2 100 hg38.150200.bed.split8694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8695 0 1 2 100 hg38.150200.bed.split8695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8696 0 1 2 100 hg38.150200.bed.split8696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8697 0 1 2 100 hg38.150200.bed.split8697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8698 0 1 2 100 hg38.150200.bed.split8698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8699 0 1 2 100 hg38.150200.bed.split8699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split87 0 1 2 100 hg38.150200.bed.split87.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split870 0 1 2 100 hg38.150200.bed.split870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8700 0 1 2 100 hg38.150200.bed.split8700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8701 0 1 2 100 hg38.150200.bed.split8701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8702 0 1 2 100 hg38.150200.bed.split8702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8703 0 1 2 100 hg38.150200.bed.split8703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8704 0 1 2 100 hg38.150200.bed.split8704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8705 0 1 2 100 hg38.150200.bed.split8705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8706 0 1 2 100 hg38.150200.bed.split8706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8707 0 1 2 100 hg38.150200.bed.split8707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8708 0 1 2 100 hg38.150200.bed.split8708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8709 0 1 2 100 hg38.150200.bed.split8709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split871 0 1 2 100 hg38.150200.bed.split871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8710 0 1 2 100 hg38.150200.bed.split8710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8711 0 1 2 100 hg38.150200.bed.split8711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8712 0 1 2 100 hg38.150200.bed.split8712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8713 0 1 2 100 hg38.150200.bed.split8713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8714 0 1 2 100 hg38.150200.bed.split8714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8715 0 1 2 100 hg38.150200.bed.split8715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8716 0 1 2 100 hg38.150200.bed.split8716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8717 0 1 2 100 hg38.150200.bed.split8717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8718 0 1 2 100 hg38.150200.bed.split8718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8719 0 1 2 100 hg38.150200.bed.split8719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split872 0 1 2 100 hg38.150200.bed.split872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8720 0 1 2 100 hg38.150200.bed.split8720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8721 0 1 2 100 hg38.150200.bed.split8721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8722 0 1 2 100 hg38.150200.bed.split8722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8723 0 1 2 100 hg38.150200.bed.split8723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8724 0 1 2 100 hg38.150200.bed.split8724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8725 0 1 2 100 hg38.150200.bed.split8725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8726 0 1 2 100 hg38.150200.bed.split8726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8727 0 1 2 100 hg38.150200.bed.split8727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8728 0 1 2 100 hg38.150200.bed.split8728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8729 0 1 2 100 hg38.150200.bed.split8729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split873 0 1 2 100 hg38.150200.bed.split873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8730 0 1 2 100 hg38.150200.bed.split8730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8731 0 1 2 100 hg38.150200.bed.split8731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8732 0 1 2 100 hg38.150200.bed.split8732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8733 0 1 2 100 hg38.150200.bed.split8733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8734 0 1 2 100 hg38.150200.bed.split8734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8735 0 1 2 100 hg38.150200.bed.split8735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8736 0 1 2 100 hg38.150200.bed.split8736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8737 0 1 2 100 hg38.150200.bed.split8737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8738 0 1 2 100 hg38.150200.bed.split8738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8739 0 1 2 100 hg38.150200.bed.split8739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split874 0 1 2 100 hg38.150200.bed.split874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8740 0 1 2 100 hg38.150200.bed.split8740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8741 0 1 2 100 hg38.150200.bed.split8741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8742 0 1 2 100 hg38.150200.bed.split8742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8743 0 1 2 100 hg38.150200.bed.split8743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8744 0 1 2 100 hg38.150200.bed.split8744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8745 0 1 2 100 hg38.150200.bed.split8745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8746 0 1 2 100 hg38.150200.bed.split8746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8747 0 1 2 100 hg38.150200.bed.split8747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8748 0 1 2 100 hg38.150200.bed.split8748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8749 0 1 2 100 hg38.150200.bed.split8749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split875 0 1 2 100 hg38.150200.bed.split875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8750 0 1 2 100 hg38.150200.bed.split8750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8751 0 1 2 100 hg38.150200.bed.split8751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8752 0 1 2 100 hg38.150200.bed.split8752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8753 0 1 2 100 hg38.150200.bed.split8753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8754 0 1 2 100 hg38.150200.bed.split8754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8755 0 1 2 100 hg38.150200.bed.split8755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8756 0 1 2 100 hg38.150200.bed.split8756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8757 0 1 2 100 hg38.150200.bed.split8757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8758 0 1 2 100 hg38.150200.bed.split8758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8759 0 1 2 100 hg38.150200.bed.split8759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split876 0 1 2 100 hg38.150200.bed.split876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8760 0 1 2 100 hg38.150200.bed.split8760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8761 0 1 2 100 hg38.150200.bed.split8761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8762 0 1 2 100 hg38.150200.bed.split8762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8763 0 1 2 100 hg38.150200.bed.split8763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8764 0 1 2 100 hg38.150200.bed.split8764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8765 0 1 2 100 hg38.150200.bed.split8765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8766 0 1 2 100 hg38.150200.bed.split8766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8767 0 1 2 100 hg38.150200.bed.split8767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8768 0 1 2 100 hg38.150200.bed.split8768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8769 0 1 2 100 hg38.150200.bed.split8769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split877 0 1 2 100 hg38.150200.bed.split877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8770 0 1 2 100 hg38.150200.bed.split8770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8771 0 1 2 100 hg38.150200.bed.split8771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8772 0 1 2 100 hg38.150200.bed.split8772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8773 0 1 2 100 hg38.150200.bed.split8773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8774 0 1 2 100 hg38.150200.bed.split8774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8775 0 1 2 100 hg38.150200.bed.split8775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8776 0 1 2 100 hg38.150200.bed.split8776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8777 0 1 2 100 hg38.150200.bed.split8777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8778 0 1 2 100 hg38.150200.bed.split8778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8779 0 1 2 100 hg38.150200.bed.split8779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split878 0 1 2 100 hg38.150200.bed.split878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8780 0 1 2 100 hg38.150200.bed.split8780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8781 0 1 2 100 hg38.150200.bed.split8781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8782 0 1 2 100 hg38.150200.bed.split8782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8783 0 1 2 100 hg38.150200.bed.split8783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8784 0 1 2 100 hg38.150200.bed.split8784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8785 0 1 2 100 hg38.150200.bed.split8785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8786 0 1 2 100 hg38.150200.bed.split8786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8787 0 1 2 100 hg38.150200.bed.split8787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8788 0 1 2 100 hg38.150200.bed.split8788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8789 0 1 2 100 hg38.150200.bed.split8789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split879 0 1 2 100 hg38.150200.bed.split879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8790 0 1 2 100 hg38.150200.bed.split8790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8791 0 1 2 100 hg38.150200.bed.split8791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8792 0 1 2 100 hg38.150200.bed.split8792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8793 0 1 2 100 hg38.150200.bed.split8793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8794 0 1 2 100 hg38.150200.bed.split8794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8795 0 1 2 100 hg38.150200.bed.split8795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8796 0 1 2 100 hg38.150200.bed.split8796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8797 0 1 2 100 hg38.150200.bed.split8797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8798 0 1 2 100 hg38.150200.bed.split8798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8799 0 1 2 100 hg38.150200.bed.split8799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split88 0 1 2 100 hg38.150200.bed.split88.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split880 0 1 2 100 hg38.150200.bed.split880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8800 0 1 2 100 hg38.150200.bed.split8800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8801 0 1 2 100 hg38.150200.bed.split8801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8802 0 1 2 100 hg38.150200.bed.split8802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8803 0 1 2 100 hg38.150200.bed.split8803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8804 0 1 2 100 hg38.150200.bed.split8804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8805 0 1 2 100 hg38.150200.bed.split8805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8806 0 1 2 100 hg38.150200.bed.split8806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8807 0 1 2 100 hg38.150200.bed.split8807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8808 0 1 2 100 hg38.150200.bed.split8808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8809 0 1 2 100 hg38.150200.bed.split8809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split881 0 1 2 100 hg38.150200.bed.split881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8810 0 1 2 100 hg38.150200.bed.split8810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8811 0 1 2 100 hg38.150200.bed.split8811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8812 0 1 2 100 hg38.150200.bed.split8812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8813 0 1 2 100 hg38.150200.bed.split8813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8814 0 1 2 100 hg38.150200.bed.split8814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8815 0 1 2 100 hg38.150200.bed.split8815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8816 0 1 2 100 hg38.150200.bed.split8816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8817 0 1 2 100 hg38.150200.bed.split8817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8818 0 1 2 100 hg38.150200.bed.split8818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8819 0 1 2 100 hg38.150200.bed.split8819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split882 0 1 2 100 hg38.150200.bed.split882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8820 0 1 2 100 hg38.150200.bed.split8820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8821 0 1 2 100 hg38.150200.bed.split8821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8822 0 1 2 100 hg38.150200.bed.split8822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8823 0 1 2 100 hg38.150200.bed.split8823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8824 0 1 2 100 hg38.150200.bed.split8824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8825 0 1 2 100 hg38.150200.bed.split8825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8826 0 1 2 100 hg38.150200.bed.split8826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8827 0 1 2 100 hg38.150200.bed.split8827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8828 0 1 2 100 hg38.150200.bed.split8828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8829 0 1 2 100 hg38.150200.bed.split8829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split883 0 1 2 100 hg38.150200.bed.split883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8830 0 1 2 100 hg38.150200.bed.split8830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8831 0 1 2 100 hg38.150200.bed.split8831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8832 0 1 2 100 hg38.150200.bed.split8832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8833 0 1 2 100 hg38.150200.bed.split8833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8834 0 1 2 100 hg38.150200.bed.split8834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8835 0 1 2 100 hg38.150200.bed.split8835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8836 0 1 2 100 hg38.150200.bed.split8836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8837 0 1 2 100 hg38.150200.bed.split8837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8838 0 1 2 100 hg38.150200.bed.split8838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8839 0 1 2 100 hg38.150200.bed.split8839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split884 0 1 2 100 hg38.150200.bed.split884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8840 0 1 2 100 hg38.150200.bed.split8840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8841 0 1 2 100 hg38.150200.bed.split8841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8842 0 1 2 100 hg38.150200.bed.split8842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8843 0 1 2 100 hg38.150200.bed.split8843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8844 0 1 2 100 hg38.150200.bed.split8844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8845 0 1 2 100 hg38.150200.bed.split8845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8846 0 1 2 100 hg38.150200.bed.split8846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8847 0 1 2 100 hg38.150200.bed.split8847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8848 0 1 2 100 hg38.150200.bed.split8848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8849 0 1 2 100 hg38.150200.bed.split8849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split885 0 1 2 100 hg38.150200.bed.split885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8850 0 1 2 100 hg38.150200.bed.split8850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8851 0 1 2 100 hg38.150200.bed.split8851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8852 0 1 2 100 hg38.150200.bed.split8852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8853 0 1 2 100 hg38.150200.bed.split8853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8854 0 1 2 100 hg38.150200.bed.split8854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8855 0 1 2 100 hg38.150200.bed.split8855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8856 0 1 2 100 hg38.150200.bed.split8856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8857 0 1 2 100 hg38.150200.bed.split8857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8858 0 1 2 100 hg38.150200.bed.split8858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8859 0 1 2 100 hg38.150200.bed.split8859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split886 0 1 2 100 hg38.150200.bed.split886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8860 0 1 2 100 hg38.150200.bed.split8860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8861 0 1 2 100 hg38.150200.bed.split8861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8862 0 1 2 100 hg38.150200.bed.split8862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8863 0 1 2 100 hg38.150200.bed.split8863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8864 0 1 2 100 hg38.150200.bed.split8864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8865 0 1 2 100 hg38.150200.bed.split8865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8866 0 1 2 100 hg38.150200.bed.split8866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8867 0 1 2 100 hg38.150200.bed.split8867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8868 0 1 2 100 hg38.150200.bed.split8868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8869 0 1 2 100 hg38.150200.bed.split8869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split887 0 1 2 100 hg38.150200.bed.split887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8870 0 1 2 100 hg38.150200.bed.split8870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8871 0 1 2 100 hg38.150200.bed.split8871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8872 0 1 2 100 hg38.150200.bed.split8872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8873 0 1 2 100 hg38.150200.bed.split8873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8874 0 1 2 100 hg38.150200.bed.split8874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8875 0 1 2 100 hg38.150200.bed.split8875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8876 0 1 2 100 hg38.150200.bed.split8876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8877 0 1 2 100 hg38.150200.bed.split8877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8878 0 1 2 100 hg38.150200.bed.split8878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8879 0 1 2 100 hg38.150200.bed.split8879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split888 0 1 2 100 hg38.150200.bed.split888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8880 0 1 2 100 hg38.150200.bed.split8880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8881 0 1 2 100 hg38.150200.bed.split8881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8882 0 1 2 100 hg38.150200.bed.split8882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8883 0 1 2 100 hg38.150200.bed.split8883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8884 0 1 2 100 hg38.150200.bed.split8884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8885 0 1 2 100 hg38.150200.bed.split8885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8886 0 1 2 100 hg38.150200.bed.split8886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8887 0 1 2 100 hg38.150200.bed.split8887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8888 0 1 2 100 hg38.150200.bed.split8888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8889 0 1 2 100 hg38.150200.bed.split8889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split889 0 1 2 100 hg38.150200.bed.split889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8890 0 1 2 100 hg38.150200.bed.split8890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8891 0 1 2 100 hg38.150200.bed.split8891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8892 0 1 2 100 hg38.150200.bed.split8892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8893 0 1 2 100 hg38.150200.bed.split8893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8894 0 1 2 100 hg38.150200.bed.split8894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8895 0 1 2 100 hg38.150200.bed.split8895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8896 0 1 2 100 hg38.150200.bed.split8896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8897 0 1 2 100 hg38.150200.bed.split8897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8898 0 1 2 100 hg38.150200.bed.split8898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8899 0 1 2 100 hg38.150200.bed.split8899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split89 0 1 2 100 hg38.150200.bed.split89.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split890 0 1 2 100 hg38.150200.bed.split890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8900 0 1 2 100 hg38.150200.bed.split8900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8901 0 1 2 100 hg38.150200.bed.split8901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8902 0 1 2 100 hg38.150200.bed.split8902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8903 0 1 2 100 hg38.150200.bed.split8903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8904 0 1 2 100 hg38.150200.bed.split8904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8905 0 1 2 100 hg38.150200.bed.split8905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8906 0 1 2 100 hg38.150200.bed.split8906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8907 0 1 2 100 hg38.150200.bed.split8907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8908 0 1 2 100 hg38.150200.bed.split8908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8909 0 1 2 100 hg38.150200.bed.split8909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split891 0 1 2 100 hg38.150200.bed.split891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8910 0 1 2 100 hg38.150200.bed.split8910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8911 0 1 2 100 hg38.150200.bed.split8911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8912 0 1 2 100 hg38.150200.bed.split8912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8913 0 1 2 100 hg38.150200.bed.split8913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8914 0 1 2 100 hg38.150200.bed.split8914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8915 0 1 2 100 hg38.150200.bed.split8915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8916 0 1 2 100 hg38.150200.bed.split8916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8917 0 1 2 100 hg38.150200.bed.split8917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8918 0 1 2 100 hg38.150200.bed.split8918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8919 0 1 2 100 hg38.150200.bed.split8919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split892 0 1 2 100 hg38.150200.bed.split892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8920 0 1 2 100 hg38.150200.bed.split8920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8921 0 1 2 100 hg38.150200.bed.split8921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8922 0 1 2 100 hg38.150200.bed.split8922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8923 0 1 2 100 hg38.150200.bed.split8923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8924 0 1 2 100 hg38.150200.bed.split8924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8925 0 1 2 100 hg38.150200.bed.split8925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8926 0 1 2 100 hg38.150200.bed.split8926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8927 0 1 2 100 hg38.150200.bed.split8927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8928 0 1 2 100 hg38.150200.bed.split8928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8929 0 1 2 100 hg38.150200.bed.split8929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split893 0 1 2 100 hg38.150200.bed.split893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8930 0 1 2 100 hg38.150200.bed.split8930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8931 0 1 2 100 hg38.150200.bed.split8931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8932 0 1 2 100 hg38.150200.bed.split8932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8933 0 1 2 100 hg38.150200.bed.split8933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8934 0 1 2 100 hg38.150200.bed.split8934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8935 0 1 2 100 hg38.150200.bed.split8935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8936 0 1 2 100 hg38.150200.bed.split8936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8937 0 1 2 100 hg38.150200.bed.split8937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8938 0 1 2 100 hg38.150200.bed.split8938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8939 0 1 2 100 hg38.150200.bed.split8939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split894 0 1 2 100 hg38.150200.bed.split894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8940 0 1 2 100 hg38.150200.bed.split8940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8941 0 1 2 100 hg38.150200.bed.split8941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8942 0 1 2 100 hg38.150200.bed.split8942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8943 0 1 2 100 hg38.150200.bed.split8943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8944 0 1 2 100 hg38.150200.bed.split8944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8945 0 1 2 100 hg38.150200.bed.split8945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8946 0 1 2 100 hg38.150200.bed.split8946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8947 0 1 2 100 hg38.150200.bed.split8947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8948 0 1 2 100 hg38.150200.bed.split8948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8949 0 1 2 100 hg38.150200.bed.split8949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split895 0 1 2 100 hg38.150200.bed.split895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8950 0 1 2 100 hg38.150200.bed.split8950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8951 0 1 2 100 hg38.150200.bed.split8951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8952 0 1 2 100 hg38.150200.bed.split8952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8953 0 1 2 100 hg38.150200.bed.split8953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8954 0 1 2 100 hg38.150200.bed.split8954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8955 0 1 2 100 hg38.150200.bed.split8955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8956 0 1 2 100 hg38.150200.bed.split8956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8957 0 1 2 100 hg38.150200.bed.split8957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8958 0 1 2 100 hg38.150200.bed.split8958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8959 0 1 2 100 hg38.150200.bed.split8959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split896 0 1 2 100 hg38.150200.bed.split896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8960 0 1 2 100 hg38.150200.bed.split8960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8961 0 1 2 100 hg38.150200.bed.split8961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8962 0 1 2 100 hg38.150200.bed.split8962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8963 0 1 2 100 hg38.150200.bed.split8963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8964 0 1 2 100 hg38.150200.bed.split8964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8965 0 1 2 100 hg38.150200.bed.split8965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8966 0 1 2 100 hg38.150200.bed.split8966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8967 0 1 2 100 hg38.150200.bed.split8967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8968 0 1 2 100 hg38.150200.bed.split8968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8969 0 1 2 100 hg38.150200.bed.split8969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split897 0 1 2 100 hg38.150200.bed.split897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8970 0 1 2 100 hg38.150200.bed.split8970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8971 0 1 2 100 hg38.150200.bed.split8971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8972 0 1 2 100 hg38.150200.bed.split8972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8973 0 1 2 100 hg38.150200.bed.split8973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8974 0 1 2 100 hg38.150200.bed.split8974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8975 0 1 2 100 hg38.150200.bed.split8975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8976 0 1 2 100 hg38.150200.bed.split8976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8977 0 1 2 100 hg38.150200.bed.split8977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8978 0 1 2 100 hg38.150200.bed.split8978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8979 0 1 2 100 hg38.150200.bed.split8979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split898 0 1 2 100 hg38.150200.bed.split898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8980 0 1 2 100 hg38.150200.bed.split8980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8981 0 1 2 100 hg38.150200.bed.split8981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8982 0 1 2 100 hg38.150200.bed.split8982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8983 0 1 2 100 hg38.150200.bed.split8983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8984 0 1 2 100 hg38.150200.bed.split8984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8985 0 1 2 100 hg38.150200.bed.split8985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8986 0 1 2 100 hg38.150200.bed.split8986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8987 0 1 2 100 hg38.150200.bed.split8987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8988 0 1 2 100 hg38.150200.bed.split8988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8989 0 1 2 100 hg38.150200.bed.split8989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split899 0 1 2 100 hg38.150200.bed.split899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8990 0 1 2 100 hg38.150200.bed.split8990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8991 0 1 2 100 hg38.150200.bed.split8991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8992 0 1 2 100 hg38.150200.bed.split8992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8993 0 1 2 100 hg38.150200.bed.split8993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8994 0 1 2 100 hg38.150200.bed.split8994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8995 0 1 2 100 hg38.150200.bed.split8995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8996 0 1 2 100 hg38.150200.bed.split8996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8997 0 1 2 100 hg38.150200.bed.split8997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8998 0 1 2 100 hg38.150200.bed.split8998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split8999 0 1 2 100 hg38.150200.bed.split8999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9 0 1 2 100 hg38.150200.bed.split9.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split90 0 1 2 100 hg38.150200.bed.split90.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split900 0 1 2 100 hg38.150200.bed.split900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9000 0 1 2 100 hg38.150200.bed.split9000.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9001 0 1 2 100 hg38.150200.bed.split9001.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9002 0 1 2 100 hg38.150200.bed.split9002.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9003 0 1 2 100 hg38.150200.bed.split9003.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9004 0 1 2 100 hg38.150200.bed.split9004.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9005 0 1 2 100 hg38.150200.bed.split9005.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9006 0 1 2 100 hg38.150200.bed.split9006.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9007 0 1 2 100 hg38.150200.bed.split9007.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9008 0 1 2 100 hg38.150200.bed.split9008.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9009 0 1 2 100 hg38.150200.bed.split9009.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split901 0 1 2 100 hg38.150200.bed.split901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9010 0 1 2 100 hg38.150200.bed.split9010.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9011 0 1 2 100 hg38.150200.bed.split9011.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9012 0 1 2 100 hg38.150200.bed.split9012.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9013 0 1 2 100 hg38.150200.bed.split9013.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9014 0 1 2 100 hg38.150200.bed.split9014.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9015 0 1 2 100 hg38.150200.bed.split9015.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9016 0 1 2 100 hg38.150200.bed.split9016.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9017 0 1 2 100 hg38.150200.bed.split9017.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9018 0 1 2 100 hg38.150200.bed.split9018.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9019 0 1 2 100 hg38.150200.bed.split9019.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split902 0 1 2 100 hg38.150200.bed.split902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9020 0 1 2 100 hg38.150200.bed.split9020.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9021 0 1 2 100 hg38.150200.bed.split9021.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9022 0 1 2 100 hg38.150200.bed.split9022.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9023 0 1 2 100 hg38.150200.bed.split9023.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9024 0 1 2 100 hg38.150200.bed.split9024.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9025 0 1 2 100 hg38.150200.bed.split9025.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9026 0 1 2 100 hg38.150200.bed.split9026.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9027 0 1 2 100 hg38.150200.bed.split9027.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9028 0 1 2 100 hg38.150200.bed.split9028.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9029 0 1 2 100 hg38.150200.bed.split9029.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split903 0 1 2 100 hg38.150200.bed.split903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9030 0 1 2 100 hg38.150200.bed.split9030.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9031 0 1 2 100 hg38.150200.bed.split9031.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9032 0 1 2 100 hg38.150200.bed.split9032.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9033 0 1 2 100 hg38.150200.bed.split9033.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9034 0 1 2 100 hg38.150200.bed.split9034.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9035 0 1 2 100 hg38.150200.bed.split9035.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9036 0 1 2 100 hg38.150200.bed.split9036.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9037 0 1 2 100 hg38.150200.bed.split9037.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9038 0 1 2 100 hg38.150200.bed.split9038.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9039 0 1 2 100 hg38.150200.bed.split9039.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split904 0 1 2 100 hg38.150200.bed.split904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9040 0 1 2 100 hg38.150200.bed.split9040.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9041 0 1 2 100 hg38.150200.bed.split9041.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9042 0 1 2 100 hg38.150200.bed.split9042.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9043 0 1 2 100 hg38.150200.bed.split9043.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9044 0 1 2 100 hg38.150200.bed.split9044.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9045 0 1 2 100 hg38.150200.bed.split9045.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9046 0 1 2 100 hg38.150200.bed.split9046.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9047 0 1 2 100 hg38.150200.bed.split9047.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9048 0 1 2 100 hg38.150200.bed.split9048.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9049 0 1 2 100 hg38.150200.bed.split9049.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split905 0 1 2 100 hg38.150200.bed.split905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9050 0 1 2 100 hg38.150200.bed.split9050.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9051 0 1 2 100 hg38.150200.bed.split9051.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9052 0 1 2 100 hg38.150200.bed.split9052.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9053 0 1 2 100 hg38.150200.bed.split9053.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9054 0 1 2 100 hg38.150200.bed.split9054.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9055 0 1 2 100 hg38.150200.bed.split9055.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9056 0 1 2 100 hg38.150200.bed.split9056.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9057 0 1 2 100 hg38.150200.bed.split9057.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9058 0 1 2 100 hg38.150200.bed.split9058.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9059 0 1 2 100 hg38.150200.bed.split9059.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split906 0 1 2 100 hg38.150200.bed.split906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9060 0 1 2 100 hg38.150200.bed.split9060.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9061 0 1 2 100 hg38.150200.bed.split9061.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9062 0 1 2 100 hg38.150200.bed.split9062.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9063 0 1 2 100 hg38.150200.bed.split9063.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9064 0 1 2 100 hg38.150200.bed.split9064.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9065 0 1 2 100 hg38.150200.bed.split9065.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9066 0 1 2 100 hg38.150200.bed.split9066.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9067 0 1 2 100 hg38.150200.bed.split9067.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9068 0 1 2 100 hg38.150200.bed.split9068.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9069 0 1 2 100 hg38.150200.bed.split9069.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split907 0 1 2 100 hg38.150200.bed.split907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9070 0 1 2 100 hg38.150200.bed.split9070.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9071 0 1 2 100 hg38.150200.bed.split9071.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9072 0 1 2 100 hg38.150200.bed.split9072.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9073 0 1 2 100 hg38.150200.bed.split9073.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9074 0 1 2 100 hg38.150200.bed.split9074.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9075 0 1 2 100 hg38.150200.bed.split9075.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9076 0 1 2 100 hg38.150200.bed.split9076.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9077 0 1 2 100 hg38.150200.bed.split9077.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9078 0 1 2 100 hg38.150200.bed.split9078.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9079 0 1 2 100 hg38.150200.bed.split9079.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split908 0 1 2 100 hg38.150200.bed.split908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9080 0 1 2 100 hg38.150200.bed.split9080.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9081 0 1 2 100 hg38.150200.bed.split9081.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9082 0 1 2 100 hg38.150200.bed.split9082.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9083 0 1 2 100 hg38.150200.bed.split9083.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9084 0 1 2 100 hg38.150200.bed.split9084.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9085 0 1 2 100 hg38.150200.bed.split9085.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9086 0 1 2 100 hg38.150200.bed.split9086.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9087 0 1 2 100 hg38.150200.bed.split9087.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9088 0 1 2 100 hg38.150200.bed.split9088.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9089 0 1 2 100 hg38.150200.bed.split9089.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split909 0 1 2 100 hg38.150200.bed.split909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9090 0 1 2 100 hg38.150200.bed.split9090.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9091 0 1 2 100 hg38.150200.bed.split9091.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9092 0 1 2 100 hg38.150200.bed.split9092.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9093 0 1 2 100 hg38.150200.bed.split9093.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9094 0 1 2 100 hg38.150200.bed.split9094.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9095 0 1 2 100 hg38.150200.bed.split9095.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9096 0 1 2 100 hg38.150200.bed.split9096.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9097 0 1 2 100 hg38.150200.bed.split9097.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9098 0 1 2 100 hg38.150200.bed.split9098.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9099 0 1 2 100 hg38.150200.bed.split9099.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split91 0 1 2 100 hg38.150200.bed.split91.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split910 0 1 2 100 hg38.150200.bed.split910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9100 0 1 2 100 hg38.150200.bed.split9100.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9101 0 1 2 100 hg38.150200.bed.split9101.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9102 0 1 2 100 hg38.150200.bed.split9102.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9103 0 1 2 100 hg38.150200.bed.split9103.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9104 0 1 2 100 hg38.150200.bed.split9104.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9105 0 1 2 100 hg38.150200.bed.split9105.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9106 0 1 2 100 hg38.150200.bed.split9106.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9107 0 1 2 100 hg38.150200.bed.split9107.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9108 0 1 2 100 hg38.150200.bed.split9108.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9109 0 1 2 100 hg38.150200.bed.split9109.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split911 0 1 2 100 hg38.150200.bed.split911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9110 0 1 2 100 hg38.150200.bed.split9110.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9111 0 1 2 100 hg38.150200.bed.split9111.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9112 0 1 2 100 hg38.150200.bed.split9112.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9113 0 1 2 100 hg38.150200.bed.split9113.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9114 0 1 2 100 hg38.150200.bed.split9114.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9115 0 1 2 100 hg38.150200.bed.split9115.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9116 0 1 2 100 hg38.150200.bed.split9116.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9117 0 1 2 100 hg38.150200.bed.split9117.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9118 0 1 2 100 hg38.150200.bed.split9118.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9119 0 1 2 100 hg38.150200.bed.split9119.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split912 0 1 2 100 hg38.150200.bed.split912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9120 0 1 2 100 hg38.150200.bed.split9120.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9121 0 1 2 100 hg38.150200.bed.split9121.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9122 0 1 2 100 hg38.150200.bed.split9122.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9123 0 1 2 100 hg38.150200.bed.split9123.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9124 0 1 2 100 hg38.150200.bed.split9124.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9125 0 1 2 100 hg38.150200.bed.split9125.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9126 0 1 2 100 hg38.150200.bed.split9126.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9127 0 1 2 100 hg38.150200.bed.split9127.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9128 0 1 2 100 hg38.150200.bed.split9128.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9129 0 1 2 100 hg38.150200.bed.split9129.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split913 0 1 2 100 hg38.150200.bed.split913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9130 0 1 2 100 hg38.150200.bed.split9130.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9131 0 1 2 100 hg38.150200.bed.split9131.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9132 0 1 2 100 hg38.150200.bed.split9132.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9133 0 1 2 100 hg38.150200.bed.split9133.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9134 0 1 2 100 hg38.150200.bed.split9134.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9135 0 1 2 100 hg38.150200.bed.split9135.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9136 0 1 2 100 hg38.150200.bed.split9136.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9137 0 1 2 100 hg38.150200.bed.split9137.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9138 0 1 2 100 hg38.150200.bed.split9138.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9139 0 1 2 100 hg38.150200.bed.split9139.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split914 0 1 2 100 hg38.150200.bed.split914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9140 0 1 2 100 hg38.150200.bed.split9140.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9141 0 1 2 100 hg38.150200.bed.split9141.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9142 0 1 2 100 hg38.150200.bed.split9142.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9143 0 1 2 100 hg38.150200.bed.split9143.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9144 0 1 2 100 hg38.150200.bed.split9144.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9145 0 1 2 100 hg38.150200.bed.split9145.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9146 0 1 2 100 hg38.150200.bed.split9146.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9147 0 1 2 100 hg38.150200.bed.split9147.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9148 0 1 2 100 hg38.150200.bed.split9148.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9149 0 1 2 100 hg38.150200.bed.split9149.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split915 0 1 2 100 hg38.150200.bed.split915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9150 0 1 2 100 hg38.150200.bed.split9150.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9151 0 1 2 100 hg38.150200.bed.split9151.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9152 0 1 2 100 hg38.150200.bed.split9152.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9153 0 1 2 100 hg38.150200.bed.split9153.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9154 0 1 2 100 hg38.150200.bed.split9154.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9155 0 1 2 100 hg38.150200.bed.split9155.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9156 0 1 2 100 hg38.150200.bed.split9156.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9157 0 1 2 100 hg38.150200.bed.split9157.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9158 0 1 2 100 hg38.150200.bed.split9158.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9159 0 1 2 100 hg38.150200.bed.split9159.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split916 0 1 2 100 hg38.150200.bed.split916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9160 0 1 2 100 hg38.150200.bed.split9160.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9161 0 1 2 100 hg38.150200.bed.split9161.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9162 0 1 2 100 hg38.150200.bed.split9162.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9163 0 1 2 100 hg38.150200.bed.split9163.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9164 0 1 2 100 hg38.150200.bed.split9164.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9165 0 1 2 100 hg38.150200.bed.split9165.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9166 0 1 2 100 hg38.150200.bed.split9166.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9167 0 1 2 100 hg38.150200.bed.split9167.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9168 0 1 2 100 hg38.150200.bed.split9168.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9169 0 1 2 100 hg38.150200.bed.split9169.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split917 0 1 2 100 hg38.150200.bed.split917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9170 0 1 2 100 hg38.150200.bed.split9170.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9171 0 1 2 100 hg38.150200.bed.split9171.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9172 0 1 2 100 hg38.150200.bed.split9172.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9173 0 1 2 100 hg38.150200.bed.split9173.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9174 0 1 2 100 hg38.150200.bed.split9174.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9175 0 1 2 100 hg38.150200.bed.split9175.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9176 0 1 2 100 hg38.150200.bed.split9176.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9177 0 1 2 100 hg38.150200.bed.split9177.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9178 0 1 2 100 hg38.150200.bed.split9178.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9179 0 1 2 100 hg38.150200.bed.split9179.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split918 0 1 2 100 hg38.150200.bed.split918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9180 0 1 2 100 hg38.150200.bed.split9180.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9181 0 1 2 100 hg38.150200.bed.split9181.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9182 0 1 2 100 hg38.150200.bed.split9182.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9183 0 1 2 100 hg38.150200.bed.split9183.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9184 0 1 2 100 hg38.150200.bed.split9184.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9185 0 1 2 100 hg38.150200.bed.split9185.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9186 0 1 2 100 hg38.150200.bed.split9186.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9187 0 1 2 100 hg38.150200.bed.split9187.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9188 0 1 2 100 hg38.150200.bed.split9188.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9189 0 1 2 100 hg38.150200.bed.split9189.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split919 0 1 2 100 hg38.150200.bed.split919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9190 0 1 2 100 hg38.150200.bed.split9190.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9191 0 1 2 100 hg38.150200.bed.split9191.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9192 0 1 2 100 hg38.150200.bed.split9192.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9193 0 1 2 100 hg38.150200.bed.split9193.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9194 0 1 2 100 hg38.150200.bed.split9194.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9195 0 1 2 100 hg38.150200.bed.split9195.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9196 0 1 2 100 hg38.150200.bed.split9196.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9197 0 1 2 100 hg38.150200.bed.split9197.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9198 0 1 2 100 hg38.150200.bed.split9198.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9199 0 1 2 100 hg38.150200.bed.split9199.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split92 0 1 2 100 hg38.150200.bed.split92.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split920 0 1 2 100 hg38.150200.bed.split920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9200 0 1 2 100 hg38.150200.bed.split9200.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9201 0 1 2 100 hg38.150200.bed.split9201.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9202 0 1 2 100 hg38.150200.bed.split9202.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9203 0 1 2 100 hg38.150200.bed.split9203.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9204 0 1 2 100 hg38.150200.bed.split9204.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9205 0 1 2 100 hg38.150200.bed.split9205.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9206 0 1 2 100 hg38.150200.bed.split9206.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9207 0 1 2 100 hg38.150200.bed.split9207.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9208 0 1 2 100 hg38.150200.bed.split9208.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9209 0 1 2 100 hg38.150200.bed.split9209.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split921 0 1 2 100 hg38.150200.bed.split921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9210 0 1 2 100 hg38.150200.bed.split9210.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9211 0 1 2 100 hg38.150200.bed.split9211.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9212 0 1 2 100 hg38.150200.bed.split9212.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9213 0 1 2 100 hg38.150200.bed.split9213.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9214 0 1 2 100 hg38.150200.bed.split9214.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9215 0 1 2 100 hg38.150200.bed.split9215.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9216 0 1 2 100 hg38.150200.bed.split9216.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9217 0 1 2 100 hg38.150200.bed.split9217.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9218 0 1 2 100 hg38.150200.bed.split9218.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9219 0 1 2 100 hg38.150200.bed.split9219.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split922 0 1 2 100 hg38.150200.bed.split922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9220 0 1 2 100 hg38.150200.bed.split9220.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9221 0 1 2 100 hg38.150200.bed.split9221.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9222 0 1 2 100 hg38.150200.bed.split9222.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9223 0 1 2 100 hg38.150200.bed.split9223.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9224 0 1 2 100 hg38.150200.bed.split9224.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9225 0 1 2 100 hg38.150200.bed.split9225.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9226 0 1 2 100 hg38.150200.bed.split9226.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9227 0 1 2 100 hg38.150200.bed.split9227.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9228 0 1 2 100 hg38.150200.bed.split9228.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9229 0 1 2 100 hg38.150200.bed.split9229.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split923 0 1 2 100 hg38.150200.bed.split923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9230 0 1 2 100 hg38.150200.bed.split9230.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9231 0 1 2 100 hg38.150200.bed.split9231.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9232 0 1 2 100 hg38.150200.bed.split9232.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9233 0 1 2 100 hg38.150200.bed.split9233.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9234 0 1 2 100 hg38.150200.bed.split9234.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9235 0 1 2 100 hg38.150200.bed.split9235.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9236 0 1 2 100 hg38.150200.bed.split9236.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9237 0 1 2 100 hg38.150200.bed.split9237.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9238 0 1 2 100 hg38.150200.bed.split9238.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9239 0 1 2 100 hg38.150200.bed.split9239.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split924 0 1 2 100 hg38.150200.bed.split924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9240 0 1 2 100 hg38.150200.bed.split9240.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9241 0 1 2 100 hg38.150200.bed.split9241.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9242 0 1 2 100 hg38.150200.bed.split9242.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9243 0 1 2 100 hg38.150200.bed.split9243.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9244 0 1 2 100 hg38.150200.bed.split9244.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9245 0 1 2 100 hg38.150200.bed.split9245.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9246 0 1 2 100 hg38.150200.bed.split9246.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9247 0 1 2 100 hg38.150200.bed.split9247.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9248 0 1 2 100 hg38.150200.bed.split9248.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9249 0 1 2 100 hg38.150200.bed.split9249.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split925 0 1 2 100 hg38.150200.bed.split925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9250 0 1 2 100 hg38.150200.bed.split9250.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9251 0 1 2 100 hg38.150200.bed.split9251.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9252 0 1 2 100 hg38.150200.bed.split9252.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9253 0 1 2 100 hg38.150200.bed.split9253.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9254 0 1 2 100 hg38.150200.bed.split9254.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9255 0 1 2 100 hg38.150200.bed.split9255.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9256 0 1 2 100 hg38.150200.bed.split9256.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9257 0 1 2 100 hg38.150200.bed.split9257.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9258 0 1 2 100 hg38.150200.bed.split9258.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9259 0 1 2 100 hg38.150200.bed.split9259.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split926 0 1 2 100 hg38.150200.bed.split926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9260 0 1 2 100 hg38.150200.bed.split9260.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9261 0 1 2 100 hg38.150200.bed.split9261.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9262 0 1 2 100 hg38.150200.bed.split9262.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9263 0 1 2 100 hg38.150200.bed.split9263.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9264 0 1 2 100 hg38.150200.bed.split9264.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9265 0 1 2 100 hg38.150200.bed.split9265.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9266 0 1 2 100 hg38.150200.bed.split9266.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9267 0 1 2 100 hg38.150200.bed.split9267.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9268 0 1 2 100 hg38.150200.bed.split9268.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9269 0 1 2 100 hg38.150200.bed.split9269.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split927 0 1 2 100 hg38.150200.bed.split927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9270 0 1 2 100 hg38.150200.bed.split9270.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9271 0 1 2 100 hg38.150200.bed.split9271.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9272 0 1 2 100 hg38.150200.bed.split9272.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9273 0 1 2 100 hg38.150200.bed.split9273.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9274 0 1 2 100 hg38.150200.bed.split9274.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9275 0 1 2 100 hg38.150200.bed.split9275.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9276 0 1 2 100 hg38.150200.bed.split9276.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9277 0 1 2 100 hg38.150200.bed.split9277.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9278 0 1 2 100 hg38.150200.bed.split9278.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9279 0 1 2 100 hg38.150200.bed.split9279.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split928 0 1 2 100 hg38.150200.bed.split928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9280 0 1 2 100 hg38.150200.bed.split9280.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9281 0 1 2 100 hg38.150200.bed.split9281.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9282 0 1 2 100 hg38.150200.bed.split9282.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9283 0 1 2 100 hg38.150200.bed.split9283.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9284 0 1 2 100 hg38.150200.bed.split9284.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9285 0 1 2 100 hg38.150200.bed.split9285.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9286 0 1 2 100 hg38.150200.bed.split9286.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9287 0 1 2 100 hg38.150200.bed.split9287.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9288 0 1 2 100 hg38.150200.bed.split9288.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9289 0 1 2 100 hg38.150200.bed.split9289.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split929 0 1 2 100 hg38.150200.bed.split929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9290 0 1 2 100 hg38.150200.bed.split9290.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9291 0 1 2 100 hg38.150200.bed.split9291.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9292 0 1 2 100 hg38.150200.bed.split9292.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9293 0 1 2 100 hg38.150200.bed.split9293.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9294 0 1 2 100 hg38.150200.bed.split9294.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9295 0 1 2 100 hg38.150200.bed.split9295.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9296 0 1 2 100 hg38.150200.bed.split9296.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9297 0 1 2 100 hg38.150200.bed.split9297.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9298 0 1 2 100 hg38.150200.bed.split9298.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9299 0 1 2 100 hg38.150200.bed.split9299.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split93 0 1 2 100 hg38.150200.bed.split93.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split930 0 1 2 100 hg38.150200.bed.split930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9300 0 1 2 100 hg38.150200.bed.split9300.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9301 0 1 2 100 hg38.150200.bed.split9301.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9302 0 1 2 100 hg38.150200.bed.split9302.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9303 0 1 2 100 hg38.150200.bed.split9303.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9304 0 1 2 100 hg38.150200.bed.split9304.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9305 0 1 2 100 hg38.150200.bed.split9305.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9306 0 1 2 100 hg38.150200.bed.split9306.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9307 0 1 2 100 hg38.150200.bed.split9307.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9308 0 1 2 100 hg38.150200.bed.split9308.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9309 0 1 2 100 hg38.150200.bed.split9309.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split931 0 1 2 100 hg38.150200.bed.split931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9310 0 1 2 100 hg38.150200.bed.split9310.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9311 0 1 2 100 hg38.150200.bed.split9311.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9312 0 1 2 100 hg38.150200.bed.split9312.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9313 0 1 2 100 hg38.150200.bed.split9313.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9314 0 1 2 100 hg38.150200.bed.split9314.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9315 0 1 2 100 hg38.150200.bed.split9315.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9316 0 1 2 100 hg38.150200.bed.split9316.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9317 0 1 2 100 hg38.150200.bed.split9317.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9318 0 1 2 100 hg38.150200.bed.split9318.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9319 0 1 2 100 hg38.150200.bed.split9319.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split932 0 1 2 100 hg38.150200.bed.split932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9320 0 1 2 100 hg38.150200.bed.split9320.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9321 0 1 2 100 hg38.150200.bed.split9321.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9322 0 1 2 100 hg38.150200.bed.split9322.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9323 0 1 2 100 hg38.150200.bed.split9323.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9324 0 1 2 100 hg38.150200.bed.split9324.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9325 0 1 2 100 hg38.150200.bed.split9325.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9326 0 1 2 100 hg38.150200.bed.split9326.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9327 0 1 2 100 hg38.150200.bed.split9327.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9328 0 1 2 100 hg38.150200.bed.split9328.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9329 0 1 2 100 hg38.150200.bed.split9329.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split933 0 1 2 100 hg38.150200.bed.split933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9330 0 1 2 100 hg38.150200.bed.split9330.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9331 0 1 2 100 hg38.150200.bed.split9331.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9332 0 1 2 100 hg38.150200.bed.split9332.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9333 0 1 2 100 hg38.150200.bed.split9333.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9334 0 1 2 100 hg38.150200.bed.split9334.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9335 0 1 2 100 hg38.150200.bed.split9335.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9336 0 1 2 100 hg38.150200.bed.split9336.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9337 0 1 2 100 hg38.150200.bed.split9337.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9338 0 1 2 100 hg38.150200.bed.split9338.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9339 0 1 2 100 hg38.150200.bed.split9339.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split934 0 1 2 100 hg38.150200.bed.split934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9340 0 1 2 100 hg38.150200.bed.split9340.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9341 0 1 2 100 hg38.150200.bed.split9341.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9342 0 1 2 100 hg38.150200.bed.split9342.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9343 0 1 2 100 hg38.150200.bed.split9343.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9344 0 1 2 100 hg38.150200.bed.split9344.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9345 0 1 2 100 hg38.150200.bed.split9345.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9346 0 1 2 100 hg38.150200.bed.split9346.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9347 0 1 2 100 hg38.150200.bed.split9347.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9348 0 1 2 100 hg38.150200.bed.split9348.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9349 0 1 2 100 hg38.150200.bed.split9349.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split935 0 1 2 100 hg38.150200.bed.split935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9350 0 1 2 100 hg38.150200.bed.split9350.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9351 0 1 2 100 hg38.150200.bed.split9351.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9352 0 1 2 100 hg38.150200.bed.split9352.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9353 0 1 2 100 hg38.150200.bed.split9353.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9354 0 1 2 100 hg38.150200.bed.split9354.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9355 0 1 2 100 hg38.150200.bed.split9355.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9356 0 1 2 100 hg38.150200.bed.split9356.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9357 0 1 2 100 hg38.150200.bed.split9357.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9358 0 1 2 100 hg38.150200.bed.split9358.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9359 0 1 2 100 hg38.150200.bed.split9359.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split936 0 1 2 100 hg38.150200.bed.split936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9360 0 1 2 100 hg38.150200.bed.split9360.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9361 0 1 2 100 hg38.150200.bed.split9361.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9362 0 1 2 100 hg38.150200.bed.split9362.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9363 0 1 2 100 hg38.150200.bed.split9363.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9364 0 1 2 100 hg38.150200.bed.split9364.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9365 0 1 2 100 hg38.150200.bed.split9365.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9366 0 1 2 100 hg38.150200.bed.split9366.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9367 0 1 2 100 hg38.150200.bed.split9367.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9368 0 1 2 100 hg38.150200.bed.split9368.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9369 0 1 2 100 hg38.150200.bed.split9369.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split937 0 1 2 100 hg38.150200.bed.split937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9370 0 1 2 100 hg38.150200.bed.split9370.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9371 0 1 2 100 hg38.150200.bed.split9371.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9372 0 1 2 100 hg38.150200.bed.split9372.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9373 0 1 2 100 hg38.150200.bed.split9373.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9374 0 1 2 100 hg38.150200.bed.split9374.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9375 0 1 2 100 hg38.150200.bed.split9375.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9376 0 1 2 100 hg38.150200.bed.split9376.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9377 0 1 2 100 hg38.150200.bed.split9377.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9378 0 1 2 100 hg38.150200.bed.split9378.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9379 0 1 2 100 hg38.150200.bed.split9379.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split938 0 1 2 100 hg38.150200.bed.split938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9380 0 1 2 100 hg38.150200.bed.split9380.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9381 0 1 2 100 hg38.150200.bed.split9381.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9382 0 1 2 100 hg38.150200.bed.split9382.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9383 0 1 2 100 hg38.150200.bed.split9383.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9384 0 1 2 100 hg38.150200.bed.split9384.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9385 0 1 2 100 hg38.150200.bed.split9385.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9386 0 1 2 100 hg38.150200.bed.split9386.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9387 0 1 2 100 hg38.150200.bed.split9387.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9388 0 1 2 100 hg38.150200.bed.split9388.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9389 0 1 2 100 hg38.150200.bed.split9389.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split939 0 1 2 100 hg38.150200.bed.split939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9390 0 1 2 100 hg38.150200.bed.split9390.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9391 0 1 2 100 hg38.150200.bed.split9391.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9392 0 1 2 100 hg38.150200.bed.split9392.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9393 0 1 2 100 hg38.150200.bed.split9393.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9394 0 1 2 100 hg38.150200.bed.split9394.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9395 0 1 2 100 hg38.150200.bed.split9395.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9396 0 1 2 100 hg38.150200.bed.split9396.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9397 0 1 2 100 hg38.150200.bed.split9397.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9398 0 1 2 100 hg38.150200.bed.split9398.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9399 0 1 2 100 hg38.150200.bed.split9399.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split94 0 1 2 100 hg38.150200.bed.split94.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split940 0 1 2 100 hg38.150200.bed.split940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9400 0 1 2 100 hg38.150200.bed.split9400.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9401 0 1 2 100 hg38.150200.bed.split9401.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9402 0 1 2 100 hg38.150200.bed.split9402.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9403 0 1 2 100 hg38.150200.bed.split9403.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9404 0 1 2 100 hg38.150200.bed.split9404.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9405 0 1 2 100 hg38.150200.bed.split9405.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9406 0 1 2 100 hg38.150200.bed.split9406.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9407 0 1 2 100 hg38.150200.bed.split9407.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9408 0 1 2 100 hg38.150200.bed.split9408.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9409 0 1 2 100 hg38.150200.bed.split9409.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split941 0 1 2 100 hg38.150200.bed.split941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9410 0 1 2 100 hg38.150200.bed.split9410.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9411 0 1 2 100 hg38.150200.bed.split9411.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9412 0 1 2 100 hg38.150200.bed.split9412.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9413 0 1 2 100 hg38.150200.bed.split9413.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9414 0 1 2 100 hg38.150200.bed.split9414.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9415 0 1 2 100 hg38.150200.bed.split9415.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9416 0 1 2 100 hg38.150200.bed.split9416.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9417 0 1 2 100 hg38.150200.bed.split9417.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9418 0 1 2 100 hg38.150200.bed.split9418.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9419 0 1 2 100 hg38.150200.bed.split9419.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split942 0 1 2 100 hg38.150200.bed.split942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9420 0 1 2 100 hg38.150200.bed.split9420.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9421 0 1 2 100 hg38.150200.bed.split9421.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9422 0 1 2 100 hg38.150200.bed.split9422.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9423 0 1 2 100 hg38.150200.bed.split9423.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9424 0 1 2 100 hg38.150200.bed.split9424.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9425 0 1 2 100 hg38.150200.bed.split9425.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9426 0 1 2 100 hg38.150200.bed.split9426.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9427 0 1 2 100 hg38.150200.bed.split9427.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9428 0 1 2 100 hg38.150200.bed.split9428.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9429 0 1 2 100 hg38.150200.bed.split9429.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split943 0 1 2 100 hg38.150200.bed.split943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9430 0 1 2 100 hg38.150200.bed.split9430.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9431 0 1 2 100 hg38.150200.bed.split9431.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9432 0 1 2 100 hg38.150200.bed.split9432.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9433 0 1 2 100 hg38.150200.bed.split9433.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9434 0 1 2 100 hg38.150200.bed.split9434.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9435 0 1 2 100 hg38.150200.bed.split9435.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9436 0 1 2 100 hg38.150200.bed.split9436.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9437 0 1 2 100 hg38.150200.bed.split9437.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9438 0 1 2 100 hg38.150200.bed.split9438.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9439 0 1 2 100 hg38.150200.bed.split9439.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split944 0 1 2 100 hg38.150200.bed.split944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9440 0 1 2 100 hg38.150200.bed.split9440.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9441 0 1 2 100 hg38.150200.bed.split9441.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9442 0 1 2 100 hg38.150200.bed.split9442.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9443 0 1 2 100 hg38.150200.bed.split9443.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9444 0 1 2 100 hg38.150200.bed.split9444.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9445 0 1 2 100 hg38.150200.bed.split9445.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9446 0 1 2 100 hg38.150200.bed.split9446.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9447 0 1 2 100 hg38.150200.bed.split9447.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9448 0 1 2 100 hg38.150200.bed.split9448.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9449 0 1 2 100 hg38.150200.bed.split9449.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split945 0 1 2 100 hg38.150200.bed.split945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9450 0 1 2 100 hg38.150200.bed.split9450.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9451 0 1 2 100 hg38.150200.bed.split9451.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9452 0 1 2 100 hg38.150200.bed.split9452.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9453 0 1 2 100 hg38.150200.bed.split9453.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9454 0 1 2 100 hg38.150200.bed.split9454.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9455 0 1 2 100 hg38.150200.bed.split9455.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9456 0 1 2 100 hg38.150200.bed.split9456.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9457 0 1 2 100 hg38.150200.bed.split9457.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9458 0 1 2 100 hg38.150200.bed.split9458.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9459 0 1 2 100 hg38.150200.bed.split9459.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split946 0 1 2 100 hg38.150200.bed.split946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9460 0 1 2 100 hg38.150200.bed.split9460.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9461 0 1 2 100 hg38.150200.bed.split9461.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9462 0 1 2 100 hg38.150200.bed.split9462.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9463 0 1 2 100 hg38.150200.bed.split9463.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9464 0 1 2 100 hg38.150200.bed.split9464.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9465 0 1 2 100 hg38.150200.bed.split9465.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9466 0 1 2 100 hg38.150200.bed.split9466.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9467 0 1 2 100 hg38.150200.bed.split9467.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9468 0 1 2 100 hg38.150200.bed.split9468.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9469 0 1 2 100 hg38.150200.bed.split9469.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split947 0 1 2 100 hg38.150200.bed.split947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9470 0 1 2 100 hg38.150200.bed.split9470.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9471 0 1 2 100 hg38.150200.bed.split9471.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9472 0 1 2 100 hg38.150200.bed.split9472.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9473 0 1 2 100 hg38.150200.bed.split9473.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9474 0 1 2 100 hg38.150200.bed.split9474.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9475 0 1 2 100 hg38.150200.bed.split9475.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9476 0 1 2 100 hg38.150200.bed.split9476.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9477 0 1 2 100 hg38.150200.bed.split9477.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9478 0 1 2 100 hg38.150200.bed.split9478.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9479 0 1 2 100 hg38.150200.bed.split9479.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split948 0 1 2 100 hg38.150200.bed.split948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9480 0 1 2 100 hg38.150200.bed.split9480.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9481 0 1 2 100 hg38.150200.bed.split9481.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9482 0 1 2 100 hg38.150200.bed.split9482.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9483 0 1 2 100 hg38.150200.bed.split9483.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9484 0 1 2 100 hg38.150200.bed.split9484.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9485 0 1 2 100 hg38.150200.bed.split9485.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9486 0 1 2 100 hg38.150200.bed.split9486.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9487 0 1 2 100 hg38.150200.bed.split9487.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9488 0 1 2 100 hg38.150200.bed.split9488.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9489 0 1 2 100 hg38.150200.bed.split9489.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split949 0 1 2 100 hg38.150200.bed.split949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9490 0 1 2 100 hg38.150200.bed.split9490.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9491 0 1 2 100 hg38.150200.bed.split9491.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9492 0 1 2 100 hg38.150200.bed.split9492.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9493 0 1 2 100 hg38.150200.bed.split9493.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9494 0 1 2 100 hg38.150200.bed.split9494.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9495 0 1 2 100 hg38.150200.bed.split9495.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9496 0 1 2 100 hg38.150200.bed.split9496.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9497 0 1 2 100 hg38.150200.bed.split9497.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9498 0 1 2 100 hg38.150200.bed.split9498.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9499 0 1 2 100 hg38.150200.bed.split9499.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split95 0 1 2 100 hg38.150200.bed.split95.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split950 0 1 2 100 hg38.150200.bed.split950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9500 0 1 2 100 hg38.150200.bed.split9500.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9501 0 1 2 100 hg38.150200.bed.split9501.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9502 0 1 2 100 hg38.150200.bed.split9502.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9503 0 1 2 100 hg38.150200.bed.split9503.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9504 0 1 2 100 hg38.150200.bed.split9504.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9505 0 1 2 100 hg38.150200.bed.split9505.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9506 0 1 2 100 hg38.150200.bed.split9506.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9507 0 1 2 100 hg38.150200.bed.split9507.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9508 0 1 2 100 hg38.150200.bed.split9508.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9509 0 1 2 100 hg38.150200.bed.split9509.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split951 0 1 2 100 hg38.150200.bed.split951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9510 0 1 2 100 hg38.150200.bed.split9510.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9511 0 1 2 100 hg38.150200.bed.split9511.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9512 0 1 2 100 hg38.150200.bed.split9512.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9513 0 1 2 100 hg38.150200.bed.split9513.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9514 0 1 2 100 hg38.150200.bed.split9514.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9515 0 1 2 100 hg38.150200.bed.split9515.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9516 0 1 2 100 hg38.150200.bed.split9516.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9517 0 1 2 100 hg38.150200.bed.split9517.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9518 0 1 2 100 hg38.150200.bed.split9518.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9519 0 1 2 100 hg38.150200.bed.split9519.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split952 0 1 2 100 hg38.150200.bed.split952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9520 0 1 2 100 hg38.150200.bed.split9520.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9521 0 1 2 100 hg38.150200.bed.split9521.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9522 0 1 2 100 hg38.150200.bed.split9522.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9523 0 1 2 100 hg38.150200.bed.split9523.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9524 0 1 2 100 hg38.150200.bed.split9524.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9525 0 1 2 100 hg38.150200.bed.split9525.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9526 0 1 2 100 hg38.150200.bed.split9526.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9527 0 1 2 100 hg38.150200.bed.split9527.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9528 0 1 2 100 hg38.150200.bed.split9528.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9529 0 1 2 100 hg38.150200.bed.split9529.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split953 0 1 2 100 hg38.150200.bed.split953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9530 0 1 2 100 hg38.150200.bed.split9530.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9531 0 1 2 100 hg38.150200.bed.split9531.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9532 0 1 2 100 hg38.150200.bed.split9532.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9533 0 1 2 100 hg38.150200.bed.split9533.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9534 0 1 2 100 hg38.150200.bed.split9534.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9535 0 1 2 100 hg38.150200.bed.split9535.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9536 0 1 2 100 hg38.150200.bed.split9536.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9537 0 1 2 100 hg38.150200.bed.split9537.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9538 0 1 2 100 hg38.150200.bed.split9538.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9539 0 1 2 100 hg38.150200.bed.split9539.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split954 0 1 2 100 hg38.150200.bed.split954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9540 0 1 2 100 hg38.150200.bed.split9540.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9541 0 1 2 100 hg38.150200.bed.split9541.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9542 0 1 2 100 hg38.150200.bed.split9542.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9543 0 1 2 100 hg38.150200.bed.split9543.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9544 0 1 2 100 hg38.150200.bed.split9544.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9545 0 1 2 100 hg38.150200.bed.split9545.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9546 0 1 2 100 hg38.150200.bed.split9546.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9547 0 1 2 100 hg38.150200.bed.split9547.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9548 0 1 2 100 hg38.150200.bed.split9548.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9549 0 1 2 100 hg38.150200.bed.split9549.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split955 0 1 2 100 hg38.150200.bed.split955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9550 0 1 2 100 hg38.150200.bed.split9550.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9551 0 1 2 100 hg38.150200.bed.split9551.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9552 0 1 2 100 hg38.150200.bed.split9552.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9553 0 1 2 100 hg38.150200.bed.split9553.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9554 0 1 2 100 hg38.150200.bed.split9554.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9555 0 1 2 100 hg38.150200.bed.split9555.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9556 0 1 2 100 hg38.150200.bed.split9556.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9557 0 1 2 100 hg38.150200.bed.split9557.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9558 0 1 2 100 hg38.150200.bed.split9558.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9559 0 1 2 100 hg38.150200.bed.split9559.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split956 0 1 2 100 hg38.150200.bed.split956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9560 0 1 2 100 hg38.150200.bed.split9560.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9561 0 1 2 100 hg38.150200.bed.split9561.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9562 0 1 2 100 hg38.150200.bed.split9562.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9563 0 1 2 100 hg38.150200.bed.split9563.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9564 0 1 2 100 hg38.150200.bed.split9564.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9565 0 1 2 100 hg38.150200.bed.split9565.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9566 0 1 2 100 hg38.150200.bed.split9566.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9567 0 1 2 100 hg38.150200.bed.split9567.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9568 0 1 2 100 hg38.150200.bed.split9568.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9569 0 1 2 100 hg38.150200.bed.split9569.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split957 0 1 2 100 hg38.150200.bed.split957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9570 0 1 2 100 hg38.150200.bed.split9570.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9571 0 1 2 100 hg38.150200.bed.split9571.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9572 0 1 2 100 hg38.150200.bed.split9572.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9573 0 1 2 100 hg38.150200.bed.split9573.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9574 0 1 2 100 hg38.150200.bed.split9574.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9575 0 1 2 100 hg38.150200.bed.split9575.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9576 0 1 2 100 hg38.150200.bed.split9576.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9577 0 1 2 100 hg38.150200.bed.split9577.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9578 0 1 2 100 hg38.150200.bed.split9578.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9579 0 1 2 100 hg38.150200.bed.split9579.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split958 0 1 2 100 hg38.150200.bed.split958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9580 0 1 2 100 hg38.150200.bed.split9580.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9581 0 1 2 100 hg38.150200.bed.split9581.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9582 0 1 2 100 hg38.150200.bed.split9582.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9583 0 1 2 100 hg38.150200.bed.split9583.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9584 0 1 2 100 hg38.150200.bed.split9584.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9585 0 1 2 100 hg38.150200.bed.split9585.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9586 0 1 2 100 hg38.150200.bed.split9586.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9587 0 1 2 100 hg38.150200.bed.split9587.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9588 0 1 2 100 hg38.150200.bed.split9588.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9589 0 1 2 100 hg38.150200.bed.split9589.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split959 0 1 2 100 hg38.150200.bed.split959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9590 0 1 2 100 hg38.150200.bed.split9590.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9591 0 1 2 100 hg38.150200.bed.split9591.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9592 0 1 2 100 hg38.150200.bed.split9592.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9593 0 1 2 100 hg38.150200.bed.split9593.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9594 0 1 2 100 hg38.150200.bed.split9594.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9595 0 1 2 100 hg38.150200.bed.split9595.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9596 0 1 2 100 hg38.150200.bed.split9596.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9597 0 1 2 100 hg38.150200.bed.split9597.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9598 0 1 2 100 hg38.150200.bed.split9598.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9599 0 1 2 100 hg38.150200.bed.split9599.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split96 0 1 2 100 hg38.150200.bed.split96.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split960 0 1 2 100 hg38.150200.bed.split960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9600 0 1 2 100 hg38.150200.bed.split9600.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9601 0 1 2 100 hg38.150200.bed.split9601.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9602 0 1 2 100 hg38.150200.bed.split9602.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9603 0 1 2 100 hg38.150200.bed.split9603.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9604 0 1 2 100 hg38.150200.bed.split9604.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9605 0 1 2 100 hg38.150200.bed.split9605.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9606 0 1 2 100 hg38.150200.bed.split9606.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9607 0 1 2 100 hg38.150200.bed.split9607.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9608 0 1 2 100 hg38.150200.bed.split9608.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9609 0 1 2 100 hg38.150200.bed.split9609.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split961 0 1 2 100 hg38.150200.bed.split961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9610 0 1 2 100 hg38.150200.bed.split9610.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9611 0 1 2 100 hg38.150200.bed.split9611.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9612 0 1 2 100 hg38.150200.bed.split9612.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9613 0 1 2 100 hg38.150200.bed.split9613.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9614 0 1 2 100 hg38.150200.bed.split9614.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9615 0 1 2 100 hg38.150200.bed.split9615.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9616 0 1 2 100 hg38.150200.bed.split9616.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9617 0 1 2 100 hg38.150200.bed.split9617.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9618 0 1 2 100 hg38.150200.bed.split9618.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9619 0 1 2 100 hg38.150200.bed.split9619.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split962 0 1 2 100 hg38.150200.bed.split962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9620 0 1 2 100 hg38.150200.bed.split9620.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9621 0 1 2 100 hg38.150200.bed.split9621.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9622 0 1 2 100 hg38.150200.bed.split9622.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9623 0 1 2 100 hg38.150200.bed.split9623.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9624 0 1 2 100 hg38.150200.bed.split9624.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9625 0 1 2 100 hg38.150200.bed.split9625.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9626 0 1 2 100 hg38.150200.bed.split9626.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9627 0 1 2 100 hg38.150200.bed.split9627.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9628 0 1 2 100 hg38.150200.bed.split9628.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9629 0 1 2 100 hg38.150200.bed.split9629.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split963 0 1 2 100 hg38.150200.bed.split963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9630 0 1 2 100 hg38.150200.bed.split9630.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9631 0 1 2 100 hg38.150200.bed.split9631.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9632 0 1 2 100 hg38.150200.bed.split9632.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9633 0 1 2 100 hg38.150200.bed.split9633.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9634 0 1 2 100 hg38.150200.bed.split9634.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9635 0 1 2 100 hg38.150200.bed.split9635.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9636 0 1 2 100 hg38.150200.bed.split9636.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9637 0 1 2 100 hg38.150200.bed.split9637.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9638 0 1 2 100 hg38.150200.bed.split9638.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9639 0 1 2 100 hg38.150200.bed.split9639.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split964 0 1 2 100 hg38.150200.bed.split964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9640 0 1 2 100 hg38.150200.bed.split9640.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9641 0 1 2 100 hg38.150200.bed.split9641.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9642 0 1 2 100 hg38.150200.bed.split9642.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9643 0 1 2 100 hg38.150200.bed.split9643.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9644 0 1 2 100 hg38.150200.bed.split9644.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9645 0 1 2 100 hg38.150200.bed.split9645.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9646 0 1 2 100 hg38.150200.bed.split9646.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9647 0 1 2 100 hg38.150200.bed.split9647.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9648 0 1 2 100 hg38.150200.bed.split9648.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9649 0 1 2 100 hg38.150200.bed.split9649.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split965 0 1 2 100 hg38.150200.bed.split965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9650 0 1 2 100 hg38.150200.bed.split9650.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9651 0 1 2 100 hg38.150200.bed.split9651.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9652 0 1 2 100 hg38.150200.bed.split9652.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9653 0 1 2 100 hg38.150200.bed.split9653.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9654 0 1 2 100 hg38.150200.bed.split9654.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9655 0 1 2 100 hg38.150200.bed.split9655.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9656 0 1 2 100 hg38.150200.bed.split9656.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9657 0 1 2 100 hg38.150200.bed.split9657.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9658 0 1 2 100 hg38.150200.bed.split9658.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9659 0 1 2 100 hg38.150200.bed.split9659.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split966 0 1 2 100 hg38.150200.bed.split966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9660 0 1 2 100 hg38.150200.bed.split9660.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9661 0 1 2 100 hg38.150200.bed.split9661.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9662 0 1 2 100 hg38.150200.bed.split9662.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9663 0 1 2 100 hg38.150200.bed.split9663.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9664 0 1 2 100 hg38.150200.bed.split9664.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9665 0 1 2 100 hg38.150200.bed.split9665.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9666 0 1 2 100 hg38.150200.bed.split9666.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9667 0 1 2 100 hg38.150200.bed.split9667.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9668 0 1 2 100 hg38.150200.bed.split9668.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9669 0 1 2 100 hg38.150200.bed.split9669.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split967 0 1 2 100 hg38.150200.bed.split967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9670 0 1 2 100 hg38.150200.bed.split9670.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9671 0 1 2 100 hg38.150200.bed.split9671.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9672 0 1 2 100 hg38.150200.bed.split9672.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9673 0 1 2 100 hg38.150200.bed.split9673.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9674 0 1 2 100 hg38.150200.bed.split9674.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9675 0 1 2 100 hg38.150200.bed.split9675.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9676 0 1 2 100 hg38.150200.bed.split9676.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9677 0 1 2 100 hg38.150200.bed.split9677.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9678 0 1 2 100 hg38.150200.bed.split9678.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9679 0 1 2 100 hg38.150200.bed.split9679.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split968 0 1 2 100 hg38.150200.bed.split968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9680 0 1 2 100 hg38.150200.bed.split9680.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9681 0 1 2 100 hg38.150200.bed.split9681.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9682 0 1 2 100 hg38.150200.bed.split9682.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9683 0 1 2 100 hg38.150200.bed.split9683.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9684 0 1 2 100 hg38.150200.bed.split9684.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9685 0 1 2 100 hg38.150200.bed.split9685.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9686 0 1 2 100 hg38.150200.bed.split9686.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9687 0 1 2 100 hg38.150200.bed.split9687.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9688 0 1 2 100 hg38.150200.bed.split9688.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9689 0 1 2 100 hg38.150200.bed.split9689.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split969 0 1 2 100 hg38.150200.bed.split969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9690 0 1 2 100 hg38.150200.bed.split9690.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9691 0 1 2 100 hg38.150200.bed.split9691.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9692 0 1 2 100 hg38.150200.bed.split9692.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9693 0 1 2 100 hg38.150200.bed.split9693.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9694 0 1 2 100 hg38.150200.bed.split9694.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9695 0 1 2 100 hg38.150200.bed.split9695.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9696 0 1 2 100 hg38.150200.bed.split9696.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9697 0 1 2 100 hg38.150200.bed.split9697.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9698 0 1 2 100 hg38.150200.bed.split9698.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9699 0 1 2 100 hg38.150200.bed.split9699.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split97 0 1 2 100 hg38.150200.bed.split97.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split970 0 1 2 100 hg38.150200.bed.split970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9700 0 1 2 100 hg38.150200.bed.split9700.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9701 0 1 2 100 hg38.150200.bed.split9701.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9702 0 1 2 100 hg38.150200.bed.split9702.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9703 0 1 2 100 hg38.150200.bed.split9703.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9704 0 1 2 100 hg38.150200.bed.split9704.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9705 0 1 2 100 hg38.150200.bed.split9705.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9706 0 1 2 100 hg38.150200.bed.split9706.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9707 0 1 2 100 hg38.150200.bed.split9707.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9708 0 1 2 100 hg38.150200.bed.split9708.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9709 0 1 2 100 hg38.150200.bed.split9709.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split971 0 1 2 100 hg38.150200.bed.split971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9710 0 1 2 100 hg38.150200.bed.split9710.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9711 0 1 2 100 hg38.150200.bed.split9711.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9712 0 1 2 100 hg38.150200.bed.split9712.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9713 0 1 2 100 hg38.150200.bed.split9713.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9714 0 1 2 100 hg38.150200.bed.split9714.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9715 0 1 2 100 hg38.150200.bed.split9715.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9716 0 1 2 100 hg38.150200.bed.split9716.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9717 0 1 2 100 hg38.150200.bed.split9717.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9718 0 1 2 100 hg38.150200.bed.split9718.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9719 0 1 2 100 hg38.150200.bed.split9719.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split972 0 1 2 100 hg38.150200.bed.split972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9720 0 1 2 100 hg38.150200.bed.split9720.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9721 0 1 2 100 hg38.150200.bed.split9721.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9722 0 1 2 100 hg38.150200.bed.split9722.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9723 0 1 2 100 hg38.150200.bed.split9723.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9724 0 1 2 100 hg38.150200.bed.split9724.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9725 0 1 2 100 hg38.150200.bed.split9725.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9726 0 1 2 100 hg38.150200.bed.split9726.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9727 0 1 2 100 hg38.150200.bed.split9727.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9728 0 1 2 100 hg38.150200.bed.split9728.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9729 0 1 2 100 hg38.150200.bed.split9729.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split973 0 1 2 100 hg38.150200.bed.split973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9730 0 1 2 100 hg38.150200.bed.split9730.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9731 0 1 2 100 hg38.150200.bed.split9731.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9732 0 1 2 100 hg38.150200.bed.split9732.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9733 0 1 2 100 hg38.150200.bed.split9733.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9734 0 1 2 100 hg38.150200.bed.split9734.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9735 0 1 2 100 hg38.150200.bed.split9735.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9736 0 1 2 100 hg38.150200.bed.split9736.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9737 0 1 2 100 hg38.150200.bed.split9737.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9738 0 1 2 100 hg38.150200.bed.split9738.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9739 0 1 2 100 hg38.150200.bed.split9739.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split974 0 1 2 100 hg38.150200.bed.split974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9740 0 1 2 100 hg38.150200.bed.split9740.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9741 0 1 2 100 hg38.150200.bed.split9741.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9742 0 1 2 100 hg38.150200.bed.split9742.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9743 0 1 2 100 hg38.150200.bed.split9743.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9744 0 1 2 100 hg38.150200.bed.split9744.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9745 0 1 2 100 hg38.150200.bed.split9745.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9746 0 1 2 100 hg38.150200.bed.split9746.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9747 0 1 2 100 hg38.150200.bed.split9747.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9748 0 1 2 100 hg38.150200.bed.split9748.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9749 0 1 2 100 hg38.150200.bed.split9749.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split975 0 1 2 100 hg38.150200.bed.split975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9750 0 1 2 100 hg38.150200.bed.split9750.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9751 0 1 2 100 hg38.150200.bed.split9751.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9752 0 1 2 100 hg38.150200.bed.split9752.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9753 0 1 2 100 hg38.150200.bed.split9753.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9754 0 1 2 100 hg38.150200.bed.split9754.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9755 0 1 2 100 hg38.150200.bed.split9755.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9756 0 1 2 100 hg38.150200.bed.split9756.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9757 0 1 2 100 hg38.150200.bed.split9757.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9758 0 1 2 100 hg38.150200.bed.split9758.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9759 0 1 2 100 hg38.150200.bed.split9759.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split976 0 1 2 100 hg38.150200.bed.split976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9760 0 1 2 100 hg38.150200.bed.split9760.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9761 0 1 2 100 hg38.150200.bed.split9761.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9762 0 1 2 100 hg38.150200.bed.split9762.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9763 0 1 2 100 hg38.150200.bed.split9763.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9764 0 1 2 100 hg38.150200.bed.split9764.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9765 0 1 2 100 hg38.150200.bed.split9765.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9766 0 1 2 100 hg38.150200.bed.split9766.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9767 0 1 2 100 hg38.150200.bed.split9767.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9768 0 1 2 100 hg38.150200.bed.split9768.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9769 0 1 2 100 hg38.150200.bed.split9769.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split977 0 1 2 100 hg38.150200.bed.split977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9770 0 1 2 100 hg38.150200.bed.split9770.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9771 0 1 2 100 hg38.150200.bed.split9771.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9772 0 1 2 100 hg38.150200.bed.split9772.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9773 0 1 2 100 hg38.150200.bed.split9773.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9774 0 1 2 100 hg38.150200.bed.split9774.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9775 0 1 2 100 hg38.150200.bed.split9775.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9776 0 1 2 100 hg38.150200.bed.split9776.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9777 0 1 2 100 hg38.150200.bed.split9777.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9778 0 1 2 100 hg38.150200.bed.split9778.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9779 0 1 2 100 hg38.150200.bed.split9779.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split978 0 1 2 100 hg38.150200.bed.split978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9780 0 1 2 100 hg38.150200.bed.split9780.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9781 0 1 2 100 hg38.150200.bed.split9781.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9782 0 1 2 100 hg38.150200.bed.split9782.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9783 0 1 2 100 hg38.150200.bed.split9783.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9784 0 1 2 100 hg38.150200.bed.split9784.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9785 0 1 2 100 hg38.150200.bed.split9785.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9786 0 1 2 100 hg38.150200.bed.split9786.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9787 0 1 2 100 hg38.150200.bed.split9787.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9788 0 1 2 100 hg38.150200.bed.split9788.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9789 0 1 2 100 hg38.150200.bed.split9789.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split979 0 1 2 100 hg38.150200.bed.split979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9790 0 1 2 100 hg38.150200.bed.split9790.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9791 0 1 2 100 hg38.150200.bed.split9791.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9792 0 1 2 100 hg38.150200.bed.split9792.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9793 0 1 2 100 hg38.150200.bed.split9793.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9794 0 1 2 100 hg38.150200.bed.split9794.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9795 0 1 2 100 hg38.150200.bed.split9795.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9796 0 1 2 100 hg38.150200.bed.split9796.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9797 0 1 2 100 hg38.150200.bed.split9797.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9798 0 1 2 100 hg38.150200.bed.split9798.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9799 0 1 2 100 hg38.150200.bed.split9799.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split98 0 1 2 100 hg38.150200.bed.split98.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split980 0 1 2 100 hg38.150200.bed.split980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9800 0 1 2 100 hg38.150200.bed.split9800.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9801 0 1 2 100 hg38.150200.bed.split9801.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9802 0 1 2 100 hg38.150200.bed.split9802.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9803 0 1 2 100 hg38.150200.bed.split9803.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9804 0 1 2 100 hg38.150200.bed.split9804.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9805 0 1 2 100 hg38.150200.bed.split9805.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9806 0 1 2 100 hg38.150200.bed.split9806.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9807 0 1 2 100 hg38.150200.bed.split9807.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9808 0 1 2 100 hg38.150200.bed.split9808.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9809 0 1 2 100 hg38.150200.bed.split9809.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split981 0 1 2 100 hg38.150200.bed.split981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9810 0 1 2 100 hg38.150200.bed.split9810.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9811 0 1 2 100 hg38.150200.bed.split9811.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9812 0 1 2 100 hg38.150200.bed.split9812.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9813 0 1 2 100 hg38.150200.bed.split9813.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9814 0 1 2 100 hg38.150200.bed.split9814.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9815 0 1 2 100 hg38.150200.bed.split9815.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9816 0 1 2 100 hg38.150200.bed.split9816.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9817 0 1 2 100 hg38.150200.bed.split9817.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9818 0 1 2 100 hg38.150200.bed.split9818.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9819 0 1 2 100 hg38.150200.bed.split9819.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split982 0 1 2 100 hg38.150200.bed.split982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9820 0 1 2 100 hg38.150200.bed.split9820.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9821 0 1 2 100 hg38.150200.bed.split9821.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9822 0 1 2 100 hg38.150200.bed.split9822.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9823 0 1 2 100 hg38.150200.bed.split9823.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9824 0 1 2 100 hg38.150200.bed.split9824.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9825 0 1 2 100 hg38.150200.bed.split9825.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9826 0 1 2 100 hg38.150200.bed.split9826.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9827 0 1 2 100 hg38.150200.bed.split9827.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9828 0 1 2 100 hg38.150200.bed.split9828.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9829 0 1 2 100 hg38.150200.bed.split9829.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split983 0 1 2 100 hg38.150200.bed.split983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9830 0 1 2 100 hg38.150200.bed.split9830.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9831 0 1 2 100 hg38.150200.bed.split9831.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9832 0 1 2 100 hg38.150200.bed.split9832.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9833 0 1 2 100 hg38.150200.bed.split9833.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9834 0 1 2 100 hg38.150200.bed.split9834.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9835 0 1 2 100 hg38.150200.bed.split9835.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9836 0 1 2 100 hg38.150200.bed.split9836.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9837 0 1 2 100 hg38.150200.bed.split9837.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9838 0 1 2 100 hg38.150200.bed.split9838.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9839 0 1 2 100 hg38.150200.bed.split9839.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split984 0 1 2 100 hg38.150200.bed.split984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9840 0 1 2 100 hg38.150200.bed.split9840.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9841 0 1 2 100 hg38.150200.bed.split9841.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9842 0 1 2 100 hg38.150200.bed.split9842.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9843 0 1 2 100 hg38.150200.bed.split9843.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9844 0 1 2 100 hg38.150200.bed.split9844.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9845 0 1 2 100 hg38.150200.bed.split9845.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9846 0 1 2 100 hg38.150200.bed.split9846.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9847 0 1 2 100 hg38.150200.bed.split9847.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9848 0 1 2 100 hg38.150200.bed.split9848.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9849 0 1 2 100 hg38.150200.bed.split9849.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split985 0 1 2 100 hg38.150200.bed.split985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9850 0 1 2 100 hg38.150200.bed.split9850.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9851 0 1 2 100 hg38.150200.bed.split9851.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9852 0 1 2 100 hg38.150200.bed.split9852.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9853 0 1 2 100 hg38.150200.bed.split9853.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9854 0 1 2 100 hg38.150200.bed.split9854.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9855 0 1 2 100 hg38.150200.bed.split9855.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9856 0 1 2 100 hg38.150200.bed.split9856.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9857 0 1 2 100 hg38.150200.bed.split9857.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9858 0 1 2 100 hg38.150200.bed.split9858.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9859 0 1 2 100 hg38.150200.bed.split9859.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split986 0 1 2 100 hg38.150200.bed.split986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9860 0 1 2 100 hg38.150200.bed.split9860.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9861 0 1 2 100 hg38.150200.bed.split9861.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9862 0 1 2 100 hg38.150200.bed.split9862.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9863 0 1 2 100 hg38.150200.bed.split9863.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9864 0 1 2 100 hg38.150200.bed.split9864.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9865 0 1 2 100 hg38.150200.bed.split9865.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9866 0 1 2 100 hg38.150200.bed.split9866.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9867 0 1 2 100 hg38.150200.bed.split9867.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9868 0 1 2 100 hg38.150200.bed.split9868.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9869 0 1 2 100 hg38.150200.bed.split9869.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split987 0 1 2 100 hg38.150200.bed.split987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9870 0 1 2 100 hg38.150200.bed.split9870.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9871 0 1 2 100 hg38.150200.bed.split9871.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9872 0 1 2 100 hg38.150200.bed.split9872.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9873 0 1 2 100 hg38.150200.bed.split9873.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9874 0 1 2 100 hg38.150200.bed.split9874.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9875 0 1 2 100 hg38.150200.bed.split9875.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9876 0 1 2 100 hg38.150200.bed.split9876.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9877 0 1 2 100 hg38.150200.bed.split9877.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9878 0 1 2 100 hg38.150200.bed.split9878.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9879 0 1 2 100 hg38.150200.bed.split9879.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split988 0 1 2 100 hg38.150200.bed.split988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9880 0 1 2 100 hg38.150200.bed.split9880.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9881 0 1 2 100 hg38.150200.bed.split9881.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9882 0 1 2 100 hg38.150200.bed.split9882.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9883 0 1 2 100 hg38.150200.bed.split9883.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9884 0 1 2 100 hg38.150200.bed.split9884.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9885 0 1 2 100 hg38.150200.bed.split9885.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9886 0 1 2 100 hg38.150200.bed.split9886.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9887 0 1 2 100 hg38.150200.bed.split9887.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9888 0 1 2 100 hg38.150200.bed.split9888.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9889 0 1 2 100 hg38.150200.bed.split9889.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split989 0 1 2 100 hg38.150200.bed.split989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9890 0 1 2 100 hg38.150200.bed.split9890.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9891 0 1 2 100 hg38.150200.bed.split9891.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9892 0 1 2 100 hg38.150200.bed.split9892.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9893 0 1 2 100 hg38.150200.bed.split9893.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9894 0 1 2 100 hg38.150200.bed.split9894.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9895 0 1 2 100 hg38.150200.bed.split9895.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9896 0 1 2 100 hg38.150200.bed.split9896.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9897 0 1 2 100 hg38.150200.bed.split9897.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9898 0 1 2 100 hg38.150200.bed.split9898.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9899 0 1 2 100 hg38.150200.bed.split9899.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split99 0 1 2 100 hg38.150200.bed.split99.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split990 0 1 2 100 hg38.150200.bed.split990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9900 0 1 2 100 hg38.150200.bed.split9900.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9901 0 1 2 100 hg38.150200.bed.split9901.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9902 0 1 2 100 hg38.150200.bed.split9902.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9903 0 1 2 100 hg38.150200.bed.split9903.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9904 0 1 2 100 hg38.150200.bed.split9904.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9905 0 1 2 100 hg38.150200.bed.split9905.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9906 0 1 2 100 hg38.150200.bed.split9906.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9907 0 1 2 100 hg38.150200.bed.split9907.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9908 0 1 2 100 hg38.150200.bed.split9908.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9909 0 1 2 100 hg38.150200.bed.split9909.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split991 0 1 2 100 hg38.150200.bed.split991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9910 0 1 2 100 hg38.150200.bed.split9910.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9911 0 1 2 100 hg38.150200.bed.split9911.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9912 0 1 2 100 hg38.150200.bed.split9912.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9913 0 1 2 100 hg38.150200.bed.split9913.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9914 0 1 2 100 hg38.150200.bed.split9914.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9915 0 1 2 100 hg38.150200.bed.split9915.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9916 0 1 2 100 hg38.150200.bed.split9916.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9917 0 1 2 100 hg38.150200.bed.split9917.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9918 0 1 2 100 hg38.150200.bed.split9918.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9919 0 1 2 100 hg38.150200.bed.split9919.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split992 0 1 2 100 hg38.150200.bed.split992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9920 0 1 2 100 hg38.150200.bed.split9920.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9921 0 1 2 100 hg38.150200.bed.split9921.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9922 0 1 2 100 hg38.150200.bed.split9922.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9923 0 1 2 100 hg38.150200.bed.split9923.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9924 0 1 2 100 hg38.150200.bed.split9924.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9925 0 1 2 100 hg38.150200.bed.split9925.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9926 0 1 2 100 hg38.150200.bed.split9926.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9927 0 1 2 100 hg38.150200.bed.split9927.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9928 0 1 2 100 hg38.150200.bed.split9928.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9929 0 1 2 100 hg38.150200.bed.split9929.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split993 0 1 2 100 hg38.150200.bed.split993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9930 0 1 2 100 hg38.150200.bed.split9930.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9931 0 1 2 100 hg38.150200.bed.split9931.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9932 0 1 2 100 hg38.150200.bed.split9932.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9933 0 1 2 100 hg38.150200.bed.split9933.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9934 0 1 2 100 hg38.150200.bed.split9934.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9935 0 1 2 100 hg38.150200.bed.split9935.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9936 0 1 2 100 hg38.150200.bed.split9936.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9937 0 1 2 100 hg38.150200.bed.split9937.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9938 0 1 2 100 hg38.150200.bed.split9938.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9939 0 1 2 100 hg38.150200.bed.split9939.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split994 0 1 2 100 hg38.150200.bed.split994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9940 0 1 2 100 hg38.150200.bed.split9940.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9941 0 1 2 100 hg38.150200.bed.split9941.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9942 0 1 2 100 hg38.150200.bed.split9942.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9943 0 1 2 100 hg38.150200.bed.split9943.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9944 0 1 2 100 hg38.150200.bed.split9944.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9945 0 1 2 100 hg38.150200.bed.split9945.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9946 0 1 2 100 hg38.150200.bed.split9946.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9947 0 1 2 100 hg38.150200.bed.split9947.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9948 0 1 2 100 hg38.150200.bed.split9948.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9949 0 1 2 100 hg38.150200.bed.split9949.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split995 0 1 2 100 hg38.150200.bed.split995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9950 0 1 2 100 hg38.150200.bed.split9950.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9951 0 1 2 100 hg38.150200.bed.split9951.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9952 0 1 2 100 hg38.150200.bed.split9952.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9953 0 1 2 100 hg38.150200.bed.split9953.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9954 0 1 2 100 hg38.150200.bed.split9954.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9955 0 1 2 100 hg38.150200.bed.split9955.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9956 0 1 2 100 hg38.150200.bed.split9956.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9957 0 1 2 100 hg38.150200.bed.split9957.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9958 0 1 2 100 hg38.150200.bed.split9958.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9959 0 1 2 100 hg38.150200.bed.split9959.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split996 0 1 2 100 hg38.150200.bed.split996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9960 0 1 2 100 hg38.150200.bed.split9960.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9961 0 1 2 100 hg38.150200.bed.split9961.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9962 0 1 2 100 hg38.150200.bed.split9962.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9963 0 1 2 100 hg38.150200.bed.split9963.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9964 0 1 2 100 hg38.150200.bed.split9964.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9965 0 1 2 100 hg38.150200.bed.split9965.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9966 0 1 2 100 hg38.150200.bed.split9966.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9967 0 1 2 100 hg38.150200.bed.split9967.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9968 0 1 2 100 hg38.150200.bed.split9968.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9969 0 1 2 100 hg38.150200.bed.split9969.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split997 0 1 2 100 hg38.150200.bed.split997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9970 0 1 2 100 hg38.150200.bed.split9970.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9971 0 1 2 100 hg38.150200.bed.split9971.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9972 0 1 2 100 hg38.150200.bed.split9972.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9973 0 1 2 100 hg38.150200.bed.split9973.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9974 0 1 2 100 hg38.150200.bed.split9974.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9975 0 1 2 100 hg38.150200.bed.split9975.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9976 0 1 2 100 hg38.150200.bed.split9976.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9977 0 1 2 100 hg38.150200.bed.split9977.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9978 0 1 2 100 hg38.150200.bed.split9978.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9979 0 1 2 100 hg38.150200.bed.split9979.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split998 0 1 2 100 hg38.150200.bed.split998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9980 0 1 2 100 hg38.150200.bed.split9980.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9981 0 1 2 100 hg38.150200.bed.split9981.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9982 0 1 2 100 hg38.150200.bed.split9982.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9983 0 1 2 100 hg38.150200.bed.split9983.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9984 0 1 2 100 hg38.150200.bed.split9984.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9985 0 1 2 100 hg38.150200.bed.split9985.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9986 0 1 2 100 hg38.150200.bed.split9986.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9987 0 1 2 100 hg38.150200.bed.split9987.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9988 0 1 2 100 hg38.150200.bed.split9988.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9989 0 1 2 100 hg38.150200.bed.split9989.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split999 0 1 2 100 hg38.150200.bed.split999.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9990 0 1 2 100 hg38.150200.bed.split9990.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9991 0 1 2 100 hg38.150200.bed.split9991.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9992 0 1 2 100 hg38.150200.bed.split9992.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9993 0 1 2 100 hg38.150200.bed.split9993.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9994 0 1 2 100 hg38.150200.bed.split9994.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9995 0 1 2 100 hg38.150200.bed.split9995.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9996 0 1 2 100 hg38.150200.bed.split9996.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9997 0 1 2 100 hg38.150200.bed.split9997.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9998 0 1 2 100 hg38.150200.bed.split9998.NMI
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa hg38.150200.bed.split9999 0 1 2 100 hg38.150200.bed.split9999.NMI